SMART MODE:

NORMAL GENOMIC

• Guertin DA, McCollum D
• Interaction between the noncatalytic region of Sid1p kinase and Cdc14p is required for full catalytic activity and localization of Sid1p.
• J Biol Chem. 2001; 276: 28185-9
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• Sid1p is a group II p21-activated kinase/germinal center kinase family member that is part of a signaling network required for cytokinesis in fission yeast. Germinal center kinases are characterized by well conserved amino-terminal catalytic domains followed by less conserved carboxyl termini. The carboxyl termini among group I germinal center kinases are moderately conserved and thought to be regulatory regions. Little is known about the carboxyl termini of group II family members. Sid1p has been shown to bind the novel protein Cdc14p; however, the functional significance of this interaction is unknown. Here we report that the carboxyl terminus of Sid1p is an essential regulatory region. Our results indicate that this region contains the binding domain for Cdc14p, and this association is required for full Sid1p catalytic activity as well as intracellular localization. Furthermore, overexpression of the carboxyl terminus of Sid1p alone compromises the signaling of cytokinesis. We conclude that Cdc14p positively regulates the Sid1p kinase by binding the noncatalytic carboxyl-terminal region of the protein.

• Tereshko V, Teplova M, Brunzelle J, Watterson DM, Egli M
• Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression.
• Nat Struct Biol. 2001; 8: 899-907
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• We have determined X-ray crystal structures with up to 1.5 A resolution of the catalytic domain of death-associated protein kinase (DAPK), the first described member of a novel family of pro-apoptotic and tumor-suppressive serine/threonine kinases. The geometry of the active site was studied in the apo form, in a complex with nonhydrolyzable AMPPnP and in a ternary complex consisting of kinase, AMPPnP and either Mg2+ or Mn2+. The structures revealed a previously undescribed water-mediated stabilization of the interaction between the lysine that is conserved in protein kinases and the beta- and gamma-phosphates of ATP, as well as conformational changes at the active site upon ion binding. Comparison between these structures and nucleotide triphosphate complexes of several other kinases disclosed a number of unique features of the DAPK catalytic domain, among which is a highly ordered basic loop in the N-terminal domain that may participate in enzyme regulation.

• Guo Y, Halfter U, Ishitani M, Zhu JK
• Molecular characterization of functional domains in the protein kinase SOS2 that is required for plant salt tolerance.
• Plant Cell. 2001; 13: 1383-400
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• The SOS3 (for SALT OVERLY SENSITIVE3) calcium binding protein and SOS2 protein kinase are required for sodium and potassium ion homeostasis and salt tolerance in Arabidopsis. We have shown previously that SOS3 interacts with and activates the SOS2 protein kinase. We report here the identification of a SOS3 binding motif in SOS2 that also serves as the kinase autoinhibitory domain. Yeast two-hybrid assays as well as in vitro binding assays revealed a 21-amino acid motif in the regulatory domain of SOS2 that is necessary and sufficient for interaction with SOS3. Database searches revealed a large family of SOS2-like protein kinases containing such a SOS3 binding motif. Using a yeast two-hybrid system, we show that these SOS2-like kinases interact with members of the SOS3 family of calcium binding proteins. Two-hybrid assays also revealed interaction between the N-terminal kinase domain and the C-terminal regulatory domain within SOS2, suggesting that the regulatory domain may inhibit kinase activity by blocking substrate access to the catalytic site. Removal of the regulatory domain of SOS2, including the SOS3 binding motif, resulted in constitutive activation of the protein kinase, indicating that the SOS3 binding motif can serve as a kinase autoinhibitory domain. Constitutively active SOS2 that is SOS3 independent also was produced by changing Thr(168) to Asp in the activation loop of the SOS2 kinase domain. Combining the Thr(168)-to-Asp mutation with the autoinhibitory domain deletion created a superactive SOS2 kinase. These results provide insights into regulation of the kinase activities of SOS2 and the SOS2 family of protein kinases.

• Amodeo P, Fraternali F, Lesk AM, Pastore A
• Modularity and homology: modelling of the titin type I modules and their interfaces.
• J Mol Biol. 2001; 311: 283-96
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• Titin is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I motifs are homologous to members of the fibronectin type 3 (Fn3) superfamily, one of the motifs most widespread in modular proteins. Fn3 domains are thought to mediate protein-protein interactions and to act as spacers. In titin, Fn3 modules are present in two different super-repeated patterns, likely to be involved in sarcomere assembly through interactions with A-band proteins. Here, we discuss results from homology modelling the whole family of Fn3 domains in titin. Homology modelling is a powerful tool that will play an increasingly important role in the post-genomic era. It is particularly useful for extending experimental structure determinations of parts of multidomain proteins that contain multiple copies of the same motif. The 3D structures of a representative titin type I domain and of other extracellular Fn3 modules were used as a template to model the structures of the 132 copies in titin. The resulting models suggest residues that contribute to the fold stability and allow us to distinguish these from residues likely to have functional importance. In particular, analysis of the models and mapping of the consensus sequence onto the 3D structure suggest putative surfaces of interaction with other proteins. From the structures of isolated modules and the pattern of conservation in the multiple alignment of the whole titin Ig and Fn3 families, it is possible to address the question of how tandem modules are assembled. Our predictions can be validated experimentally. Copyright 2001 Academic Press.

• Song Y, Cohler AN, Weinstein DC
• Regulation of Laloo by the Xenopus C-terminal Src kinase (Xcsk) during early vertebrate development.
• Oncogene. 2001; 20: 5210-4
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• Mesoderm formation in the frog, Xenopus laevis, is dependent on the activity of one or more members of the Src family kinases; the molecular interactions underlying this requirement are not well understood. The C-terminal Src Kinase (Csk) is a potent inhibitor of Src activity, and is required for normal mammalian development; here we report the characterization of Xenopus Csk (Xcsk). Xcsk is widely expressed during early development, physically interacts with the Src kinase Laloo, and inhibits the generation of mesoderm by the Src kinases. Xcsk activity requires a functional kinase domain; furthermore, a kinase-inactive Xcsk mutant potently synergizes with Laloo during early vertebrate development, suggesting a fundamental role for the Src kinase-Csk regulatory circuit during mesoderm induction, in vivo.

• Kieschnick H, Wakefield T, Narducci CA, Beckers C
• Toxoplasma gondii attachment to host cells is regulated by a calmodulin-like domain protein kinase.
• J Biol Chem. 2001; 276: 12369-77
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• The role of calcium-dependent protein kinases in the invasion of Toxoplasma gondii into its animal host cells was analyzed. KT5926, an inhibitor of calcium-dependent protein kinases in other systems, is known to block the motility of Toxoplasma tachyzoites and their attachment to host cells. In vivo, KT5926 blocks the phosphorylation of only three parasite proteins, and in parasite extracts only a single KT5926-sensitive protein kinase activity was detected. This activity was calcium-dependent but did not require calmodulin. In a search for calcium-dependent protein kinases in Toxoplasma, two members of the class of calmodulin-like domain protein kinases (CDPKs) were detected. TgCDPK2 was only expressed at the mRNA level in tachyzoites, but no protein was detected. TgCDPK1 protein was expressed in Toxoplasma tachyzoites and cofractionated precisely with the peak of KT5926-sensitive protein kinase activity. TgCDPK1 kinase activity was calcium-dependent but did not require calmodulin or phospholipids. TgCDPK1 was found to be inhibited effectively by KT5926 at concentrations that block parasite attachment to host cells. In vitro, TgCDPK1 phosphorylated three parasite proteins that migrated identical to the three KT5926-sensitive phosphoproteins detected in vivo. Based on these observations, a central role is suggested for TgCDPK1 in regulating Toxoplasma motility and host cell invasion.

• Riazanova LV, Pavur KS, Petrov AN, Dorovkov MV, Riazanov AG
• [Novel type of signaling molecules: protein kinases covalently linked to ion channels]
• Mol Biol (Mosk). 2001; 35: 321-32
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• Recently we identified a new class of protein kinases with a novel type of catalytic domain structurally and evolutionarily unrelated to the conventional eukaryotic protein kinases. This new class, which we named alpha-kinases, is represented by eukaryotic elongation factor-2 kinase and the Dictyostelium myosin heavy chain kinases. Here we cloned, sequenced and analyzed the tissue distribution of five new putative mammalian alpha-kinases: melanoma alpha-kinase, kidney alpha-kinase, heart alpha-kinase, skeletal muscle alpha-kinase, and lymphocyte alpha-kinase. All five are large proteins of more than 1000 amino acids with an alpha-kinase catalytic domain located at the very carboxyl-terminus. We expressed the catalytic domain of melanoma alpha-kinase in Escherichia coli, and found that it autophosphorylates on threonine residues, demonstrating that it is a genuine protein kinase. Unexpectedly, we found that the long amino-terminal portions of melanoma and kidney alpha-kinases represent new members of the transient receptor potential (TRP) ion channel family, which are implicated in the mediation of capacitative Ca2+ entry in nonexcitable mammalian cells. This suggests that melanoma and kidney alpha-kinases, which represent a novel type of signaling molecule, are involved in the regulation of Ca2+ influx in mammalian cells.

• Till JH, Ablooglu AJ, Frankel M, Bishop SM, Kohanski RA, Hubbard SR
• Crystallographic and solution studies of an activation loop mutant of the insulin receptor tyrosine kinase: insights into kinase mechanism.
• J Biol Chem. 2001; 276: 10049-55
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• The tyrosine kinase domain of the insulin receptor is subject to autoinhibition in the unphosphorylated basal state via steric interactions involving the activation loop. A mutation in the activation loop designed to relieve autoinhibition, Asp-1161 --> Ala, substantially increases the ability of the unphosphorylated kinase to bind ATP. The crystal structure of this mutant in complex with an ATP analog has been determined at 2.4-A resolution. The structure shows that the active site is unobstructed, but the end of the activation loop is disordered and therefore the binding site for peptide substrates is not fully formed. In addition, Phe-1151 of the protein kinase-conserved DFG motif, at the beginning of the activation loop, hinders closure of the catalytic cleft and proper positioning of alpha-helix C for catalysis. These results, together with viscometric kinetic measurements, suggest that peptide substrate binding induces a reconfiguration of the unphosphorylated activation loop prior to the catalytic step. The crystallographic and solution studies provide new insights into the mechanism by which the activation loop controls phosphoryl transfer as catalyzed by the insulin receptor.

• Wybenga-Groot LE, Baskin B, Ong SH, Tong J, Pawson T, Sicheri F
• Structural basis for autoinhibition of the ephb2 receptor tyrosine kinase by the unphosphorylated juxtamembrane region.
• Cell. 2001; 106: 745-57
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• The Eph receptor tyrosine kinase family is regulated by autophosphorylation within the juxtamembrane region and the kinase activation segment. We have solved the X-ray crystal structure to 1.9 A resolution of an autoinhibited, unphosphorylated form of EphB2 comprised of the juxtamembrane region and the kinase domain. The structure, supported by mutagenesis data, reveals that the juxtamembrane segment adopts a helical conformation that distorts the small lobe of the kinase domain, and blocks the activation segment from attaining an activated conformation. Phosphorylation of conserved juxtamembrane tyrosines would relieve this autoinhibition by disturbing the association of the juxtamembrane segment with the kinase domain, while liberating phosphotyrosine sites for binding SH2 domains of target proteins. We propose that the autoinhibitory mechanism employed by EphB2 is a more general device through which receptor tyrosine kinases are controlled.

• Fieulaine S et al.
• X-ray structure of HPr kinase: a bacterial protein kinase with a P-loop nucleotide-binding domain.
• EMBO J. 2001; 20: 3917-27
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• HPr kinase/phosphatase (HprK/P) is a key regulatory enzyme controlling carbon metabolism in Gram- positive bacteria. It catalyses the ATP-dependent phosphorylation of Ser46 in HPr, a protein of the phosphotransferase system, and also its dephosphorylation. HprK/P is unrelated to eukaryotic protein kinases, but contains the Walker motif A characteristic of nucleotide-binding proteins. We report here the X-ray structure of an active fragment of Lactobacillus casei HprK/P at 2.8 A resolution, solved by the multiwavelength anomalous dispersion method on a seleniated protein (PDB code 1jb1). The protein is a hexamer, with each subunit containing an ATP-binding domain similar to nucleoside/nucleotide kinases, and a putative HPr-binding domain unrelated to the substrate-binding domains of other kinases. The Walker motif A forms a typical P-loop which binds inorganic phosphate in the crystal. We modelled ATP binding by comparison with adenylate kinase, and designed a tentative model of the complex with HPr based on a docking simulation. The results confirm that HprK/P represents a new family of protein kinases, first identified in bacteria, but which may also have members in eukaryotes.

• Yamaguchi H, Matsushita M, Nairn AC, Kuriyan J
• Crystal structure of the atypical protein kinase domain of a TRP channel with phosphotransferase activity.
• Mol Cell. 2001; 7: 1047-57
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• Transient receptor potential (TRP) channels modulate calcium levels in eukaryotic cells in response to external signals. A novel transient receptor potential channel has the ability to phosphorylate itself and other proteins on serine and threonine residues. The catalytic domain of this channel kinase has no detectable sequence similarity to classical eukaryotic protein kinases and is essential for channel function. The structure of the kinase domain, reported here, reveals unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains. The inclusion of the channel kinase catalytic domain within the eukaryotic protein kinase superfamily indicates a significantly wider distribution for this group of signaling proteins than suggested previously by sequence comparisons alone.

• Machius M, Chuang JL, Wynn RM, Tomchick DR, Chuang DT
• From the Cover: Structure of rat BCKD kinase: Nucleotide-induced domain communication in a mitochondrial protein kinase.
• Proc Natl Acad Sci U S A. 2001; 98: 11218-23
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• Mitochondrial protein kinases (mPKs) are molecular switches that down-regulate the oxidation of branched-chain alpha-ketoacids and pyruvate. Elevated levels of these metabolites are implicated in disease states such as insulin-resistant Type II diabetes, branched-chain ketoaciduria, and primary lactic acidosis. We report a three-dimensional structure of a member of the mPK family, rat branched-chain alpha-ketoacid dehydrogenase kinase (BCK). BCK features a characteristic nucleotide-binding domain and a four-helix bundle domain. These two domains are reminiscent of modules found in protein histidine kinases (PHKs), which are involved in two-component signal transduction systems. Unlike PHKs, BCK dimerizes through direct interaction of two opposing nucleotide-binding domains. Nucleotide binding to BCK is uniquely mediated by both potassium and magnesium. Binding of ATP induces disorder-order transitions in a loop region at the nucleotide-binding site. These structural changes lead to the formation of a quadruple aromatic stack in the interface between the nucleotide-binding domain and the four-helix bundle domain, where they induce a movement of the top portion of two helices. Phosphotransfer induces further ordering of the loop region, effectively trapping the reaction product ADP, which explains product inhibition in mPKs. The BCK structure is a prototype for all mPKs and will provide a framework for structure-assisted inhibitor design for this family of kinases.

• Miller M, Ginalski K, Lesyng B, Nakaigawa N, Schmidt L, Zbar B
• Structural basis of oncogenic activation caused by point mutations in the kinase domain of the MET proto-oncogene: modeling studies.
• Proteins. 2001; 44: 32-43
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• Missense mutations in the tyrosine kinase domain of the MET proto-oncogene occur in selected cases of papillary renal carcinoma. In biochemical and biological assays, these mutations produced constitutive activation of the MET kinase and led to tumor formation in nude mice. Some mutations caused transformation of NIH 3T3 cells. To elucidate the mechanism of ligand-independent MET kinase activation by point mutations, we constructed several 3D models of the wild-type and mutated MET catalytic core domains. Analysis of these structures showed that some mutations (e.g., V1110I, Y1248H/D/C, M1268T) directly alter contacts between residues from the activation loop in its inhibitory conformation and those from the main body of the catalytic domain; others (e.g., M1149T, L1213V) increase flexibility at the critical points of the tertiary structure and facilitate subdomain movements. Mutation D1246N plays a role in stabilizing the active form of the enzyme. Mutation M1268T affects the S+1 and S+3 substrate-binding pockets. Models implicate that although these changes do not compromise the affinity toward the C-terminal autophosphorylation site of the MET protein, they allow for binding of the substrate for the c-Abl tyrosine kinase. We provide biochemical data supporting this observation. Mutation L1213V affects the conformation of Tyr1212 in the active form of MET. Several somatic mutations are clustered at the surface of the catalytic domain in close vicinity of the probable location of the MET C-terminal docking site for cytoplasmic effectors. Copyright 2001 Wiley-Liss, Inc.

• Sturany S et al.
• Molecular cloning and characterization of the human protein kinase D2. A novel member of the protein kinase D family of serine threonine kinases.
• J Biol Chem. 2001; 276: 3310-8
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• We have isolated the full-length cDNA of a novel human serine threonine protein kinase gene. The deduced protein sequence contains two cysteine-rich motifs at the N terminus, a pleckstrin homology domain, and a catalytic domain containing all the characteristic sequence motifs of serine protein kinases. It exhibits the strongest homology to the serine threonine protein kinases PKD/PKC&mgr; and PKCnu, particularly in the duplex zinc finger-like cysteine-rich motif, in the pleckstrin homology domain and in the protein kinase domain. In contrast, it shows only a low degree of sequence similarity to other members of the PKC family. Therefore, the new protein has been termed protein kinase D2 (PKD2). The mRNA of PKD2 is widely expressed in human and murine tissues. It encodes a protein with a molecular mass of 105 kDa in SDS-polyacrylamide gel electrophoresis, which is expressed in various human cell lines, including HL60 cells, which do not express PKC&mgr;. In vivo phorbol ester binding studies demonstrated a concentration-dependent binding of [(3)H]phorbol 12,13-dibutyrate to PKD2. The addition of phorbol 12,13-dibutyrate in the presence of dioleoylphosphatidylserine stimulated the autophosphorylation of PKD2 in a synergistic fashion. Phorbol esters also stimulated autophosphorylation of PKD2 in intact cells. PKD2 activated by phorbol esters efficiently phosphorylated the exogenous substrate histone H1. In addition, we could identify the C-terminal Ser(876) residue as an in vivo phosphorylation site within PKD2. Phosphorylation of Ser(876) of PKD2 correlated with the activation status of the kinase. Finally, gastrin was found to be a physiological activator of PKD2 in human AGS-B cells stably transfected with the CCK(B)/gastrin receptor. Thus, PKD2 is a novel phorbol ester- and growth factor-stimulated protein kinase.

• Williams DM, Cole PA
• Kinase chips hit the proteomics era.
• Trends Biochem Sci. 2001; 26: 271-3
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• Protein kinase chips, in which kinases are tested for their ability to phosphorylate immobilized substrates, have been developed and used to evaluate the protein kinases encoded by the yeast genome. This new technology promises to be a valuable addition to the biochemists' and cell biologists' arsenal for evaluating the substrate selectivity and function of protein kinases in cell signaling.

• Xu B, English JM, Wilsbacher JL, Stippec S, Goldsmith EJ, Cobb MH
• WNK1, a novel mammalian serine/threonine protein kinase lacking the catalytic lysine in subdomain II.
• J Biol Chem. 2000; 275: 16795-801
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• We have cloned and characterized a novel mammalian serine/threonine protein kinase WNK1 (with no lysine (K)) from a rat brain cDNA library. WNK1 has 2126 amino acids and can be detected as a protein of approximately 230 kDa in various cell lines and rat tissues. WNK1 contains a small N-terminal domain followed by the kinase domain and a long C-terminal tail. The WNK1 kinase domain has the greatest similarity to the MEKK protein kinase family. However, overexpression of WNK1 in HEK293 cells exerts no detectable effect on the activity of known, co-transfected mitogen-activated protein kinases, suggesting that it belongs to a distinct pathway. WNK1 phosphorylates the exogenous substrate myelin basic protein as well as itself mostly on serine residues, confirming that it is a serine/threonine protein kinase. The demonstration of activity was striking because WNK1, and its homologs in other organisms lack the invariant catalytic lysine in subdomain II of protein kinases that is crucial for binding to ATP. A model of WNK1 using the structure of cAMP-dependent protein kinase suggests that lysine 233 in kinase subdomain I may provide this function. Mutation of this lysine residue to methionine eliminates WNK1 activity, consistent with the conclusion that it is required for catalysis. This distinct organization of catalytic residues indicates that WNK1 belongs to a novel family of serine/threonine protein kinases.

• Wetterauer BW
• Protein kinases from Dictyostelium discoideum with similarity to LIM kinases.
• Biochim Biophys Acta. 2000; 1480: 377-83
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• We cloned a protein kinase (DdKinY) from Dictyostelium discoideum by low stringency hybridization using the catalytic domain from DdKinX [B.W. Wetterauer et al., Biochim. Biophys. Acta 1265 (1995) 97-101] as a probe. Both kinases have low sequence similarity to other protein kinases in the databases. However, phylogenetic analysis showed that both kinases cluster with vertebrate LIM kinases due to homology within the catalytic domain.

• Shewchuk LM et al.
• Structure of the Tie2 RTK domain: self-inhibition by the nucleotide binding loop, activation loop, and C-terminal tail.
• Structure Fold Des. 2000; 8: 1105-13
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• BACKGROUND: Angiogenesis, the formation of new vessels from the existing vasculature, is a critical process during early development as well as in a number of disease processes. Tie2 (also known as Tek) is an endothelium-specific receptor tyrosine kinase involved in both angiogenesis and vasculature maintenance. RESULTS: We have determined the crystal structure of the Tie2 kinase domain to 2.2 A resolution. The structure contains the catalytic core, the kinase insert domain (KID), and the C-terminal tail. The overall fold is similar to that observed in other serine/threonine and tyrosine kinase structures; however, several unique features distinguish the Tie2 structure from those of other kinases. The Tie2 nucleotide binding loop is in an inhibitory conformation, which is not seen in other kinase structures, while its activation loop adopts an "activated-like" conformation in the absence of phosphorylation. Tyr-897, located in the N-terminal domain, may negatively regulate the activity of Tie2 by preventing dimerization of the kinase domains or by recruiting phosphatases when it is phosphorylated. CONCLUSION: Regulation of the kinase activity of Tie2 is a complex process. Conformational changes in the nucleotide binding loop, activation loop, C helix, and the C-terminal tail are required for ATP and substrate binding.

• Koretke KK, Lupas AN, Warren PV, Rosenberg M, Brown JR
• Evolution of two-component signal transduction.
• Mol Biol Evol. 2000; 17: 1956-70
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• Two-component signal transduction (TCST) systems are the principal means for coordinating responses to environmental changes in bacteria as well as some plants, fungi, protozoa, and archaea. These systems typically consist of a receptor histidine kinase, which reacts to an extracellular signal by phosphorylating a cytoplasmic response regulator, causing a change in cellular behavior. Although several model systems, including sporulation and chemotaxis, have been extensively studied, the evolutionary relationships between specific TCST systems are not well understood, and the ancestry of the signal transduction components is unclear. Phylogenetic trees of TCST components from 14 complete and 6 partial genomes, containing 183 histidine kinases and 220 response regulators, were constructed using distance methods. The trees showed extensive congruence in the positions of 11 recognizable phylogenetic clusters. Eukaryotic sequences were found almost exclusively in one cluster, which also showed the greatest extent of domain variability in its component proteins, and archaeal sequences mainly formed species-specific clusters. Three clusters in different parts of the kinase tree contained proteins with serine-phosphorylating activity. All kinases were found to be monophyletic with respect to other members of their superfamily, such as type II topoisomerases and Hsp90. Structural analysis further revealed significant similarity to the ATP-binding domain of eukaryotic protein kinases. TCST systems are of bacterial origin and radiated into archaea and eukaryotes by lateral gene transfer. Their components show extensive coevolution, suggesting that recombination has not been a major factor in their differentiation. Although histidine kinase activity is prevalent, serine kinases have evolved multiple times independently within this family, accompanied by a loss of the cognate response regulator(s). The structural and functional similarity between TCST kinases and eukaryotic protein kinases raises the possibility of a distant evolutionary relationship.

• Rausch O et al.
• Nerve injury-associated kinase: a sterile 20-like protein kinase up-regulated in dorsal root ganglia in a rat model of neuropathic pain.
• Neuroscience. 2000; 101: 767-77
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• Partial injury of the rat sciatic nerve elicits a variety of characteristic chemical, electrophysical and anatomical changes in primary sensory neurons and constitutes a physiologically relevant model of neuropathic pain. To elucidate molecular mechanisms that underlie the physiology of neuropathic pain, we have used messenger RNA differential display to identify genes that exhibit increased ipsilateral expression in L4/5 dorsal root ganglia, following unilateral partial ligation of the rat sciatic nerve. One set of partial complementary DNA clones identified in this screen was found to encode a protein kinase, nerve injury-associated kinase. Cloning of the full-length human nerve injury-associated kinase complementary DNA, together with recombinant expression analysis, reveal nerve injury-associated kinase to be a functional member of a subgroup of sterile 20-like protein kinases characterised by the presence of a putative carboxy terminal autoregulatory domain. Induction of nerve injury-associated kinase expression in dorsal root ganglia in the rat neuropathic pain model was confirmed by quantitative reverse transcription-polymerase chain reaction, and RNA in situ hybridization analysis revealed enhanced levels of nerve injury-associated kinase within neurons.Together, our data implicate nerve injury-associated kinase as a novel upstream component of an intracellular signalling cascade that is up-regulated in dorsal root ganglia neurons in response to sciatic nerve injury.

• Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H
• Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily.
• Structure Fold Des. 2000; 8: 1247-57
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• BACKGROUND: Homoserine kinase (HSK) catalyzes an important step in the threonine biosynthesis pathway. It belongs to a large yet unique class of small metabolite kinases, the GHMP kinase superfamily. Members in the GHMP superfamily participate in several essential metabolic pathways, such as amino acid biosynthesis, galactose metabolism, and the mevalonate pathway. RESULTS: The crystal structure of HSK and its complex with ADP reveal a novel nucleotide binding fold. The N-terminal domain contains an unusual left-handed betaalphabeta unit, while the C-terminal domain has a central alpha-beta plait fold with an insertion of four helices. The phosphate binding loop in HSK is distinct from the classical P loops found in many ATP/GTP binding proteins. The bound ADP molecule adopts a rare syn conformation and is in the opposite orientation from those bound to the P loop-containing proteins. Inspection of the substrate binding cavity indicates several amino acid residues that are likely to be involved in substrate binding and catalysis. CONCLUSIONS: The crystal structure of HSK is the first representative in the GHMP superfamily to have determined structure. It provides insight into the structure and nucleotide binding mechanism of not only the HSK family but also a variety of enzymes in the GHMP superfamily. Such enzymes include galactokinases, mevalonate kinases, phosphomevalonate kinases, mevalonate pyrophosphate decarboxylases, and several proteins of yet unknown functions.

• Enke DA, Kaldis P, Holmes JK, Solomon MJ
• The CDK-activating kinase (Cak1p) from budding yeast has an unusual ATP-binding pocket.
• J Biol Chem. 1999; 274: 1949-56
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• Cak1p is an essential protein kinase that phosphorylates and thereby activates the major cyclin-dependent kinase in budding yeast, Cdc28p. The sequence of Cak1p differs from other members of the protein kinase superfamily in several conserved regions. Cak1p lacks the highly conserved glycine loop motif (GXGXXG) that is found in the nucleotide binding fold of virtually all protein kinases and also lacks a number of conserved amino acids found at sites throughout the protein kinase core sequence. We have used kinetic and mutagenic analyses to investigate whether these sequence differences affect the nucleotide-binding properties of Cak1p. Although Cak1p differs dramatically from other protein kinases, it binds ATP with a reasonable affinity, with a KM of 4.8 microM. Mutations of the putative invariant lysine in Cak1p (Lys-31), homologous to a residue required for activity in virtually all protein kinases and that interacts with the ATP phosphates, moderately reduced the ability of Cak1p to bind ATP but did not dramatically affect the catalytic rate of the kinase. Similarly, Cak1p is insensitive to the ATP analog 5'-fluorosulfonylbenzoyladenosine, which inhibits most protein kinases through covalent modification of the invariant lysine. We found that Cak1p is tolerant of mutations within its glycine loop region. Remarkably, Cak1p remains functional even following truncation of its first 31 amino acids, including the glycine loop region and the invariant lysine. We conclude that the Cak1p nucleotide-binding pocket differs significantly from those of most other protein kinases and therefore might provide a specific target for an inhibitory drug.

• Bishop AC, Shokat KM
• Acquisition of inhibitor-sensitive protein kinases through protein design.
• Pharmacol Ther. 1999; 82: 337-46
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• Protein phosphorylation is the major post-translational modification used by eukaryotic cells to control cellular signaling. Protein kinases have emerged as attractive drug targets because heightened protein kinase activity has been associated with several proliferative diseases, most notably cancer and restenosis. Until now, it has been very difficult to confirm the utility of protein kinases as inhibitor targets because very few small molecules that selectively inhibit one particular kinase are known. Discovery of highly specific kinase inhibitors has been slow because the protein family contains approximately 2000 members, all of which share a conserved active site fold. Recent work in several laboratories has sought to circumvent the problem of kinase structural degeneracy by engineering drug sensitivity into Src family tyrosine kinases and mitogen-activated protein kinases through site-directed mutagenesis. By introducing a unique non-naturally occurring amino acid into a conserved region of the enzyme's binding site, a target protein kinase can be rapidly sensitized to a small molecule. Introduction of the engineered kinase into a cell line or animal model should greatly expedite the investigation of protein kinase inhibition as a viable drug treatment. The purpose of this review is to summarize these recent advances in protein kinase drug sensitization.

• Shtonda BB, Ostapchenko LI, Kucherenko ME
• Protein kinases, regulated by calcium and calmodulin: their structure, regulation and cellular functions.
• Ukr Biokhim Zh. 1999; 71: 5-12
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• In this review we summarize and generalize the recent data on structure, regulation and physiological role of calcium/calmodulin-dependent protein kinases, or CaM kinases. CaM kinases are the family of structurally homologous enzymes, involved into a variety of Ca(2+)-induced cellular reactions through phosphorylation of target proteins. In recent years the quantity of these enzymes has exceeded twenty, mainly due to identification of new isozymic forms of already known CaM kinases. Using crystal structure analysis data, some researchers constructed molecular models of regulation and functioning of CaM kinases. Many reports of recent years are devoted to investigation of functions of CaM kinase isozymes and their role in various cellular processes.

• Sowadski JM, Epstein LF, Lankiewicz L, Karlsson R
• Conformational diversity of catalytic cores of protein kinases.
• Pharmacol Ther. 1999; 82: 157-64
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• X-ray crystallography of the protein kinase family has provided an impressive array of crystal structures, setting the stage for rational design of specific inhibitors of these vitally important regulators of the signaling pathways of the cell. Initial work on the first crystal structure of a protein kinase, cyclic AMP-dependent protein kinase, has provided evidence of conformational changes suggested to be critical for the common catalytic event of transferring the gamma phosphate from ATP onto the targeted protein. This review updates the current status of the extent of conformational diversity of the protein kinase family and suggests that both the nature and the extent of those changes can provide a rationale for the increased occurrence of specific protein kinase inhibitors targeted at the ATP-binding site. It focuses on the fact that in addition to the sequence diversities in ATP binding clefts reported recently, there is conformational diversity in the beta sheets of the upper domains of the catalytic cores. This difference is directly related to the regulation of kinases by multiple mechanisms.

• Becker W, Joost HG
• Structural and functional characteristics of Dyrk, a novel subfamily of protein kinases with dual specificity.
• Prog Nucleic Acid Res Mol Biol. 1999; 62: 1-17
• Display abstract

• Dyrk-related kinases represent a novel subfamily of protein kinases with unique structural and enzymatic features. Its members have been identified in distantly related organisms. The yeast kinase, Yak1, has been characterized as a negative regulator of growth. Mnb from Drosophila is encoded by the minibrain gene, whose mutation results in specific defects in neurogenesis. Its mammalian homolog, Dyrk1A, is activated by tyrosine phosphorylation in the activation loop between subdomains VII and VIII of the catalytic domain. The human gene for Dyrk1A is located in the "Down syndrome critical region" of chromosome 21 and is therefore a candidate gene for mental retardation in Down syndrome. More recently, six additional mammalian Dyrk-related kinases have been identified (Dyrk1B, Dyrk1C, Dyrk2, Dyrk3, Dyrk4A, and Dyrk4B). All members of the Dyrk family contain in the activation loop the tyrosines that are essential for the full activity of Dyrk1A. Outside their catalytic domains, Dyrk kinases exhibit little sequence similarity except for a small segment immediately preceding the catalytic domain (DH-box, Dyrk homology box). An unusual enzymatic property of Dyrk-related kinases is their ability to catalyze tyrosine-directed autophosphorylation as well as phosphorylation of serine/threonine residues in exogenous substrates. The exact cellular function of the Dyrk kinases is yet unknown. However, it appears reasonable to assume that they are involved in the regulation of cellular growth and/or development.

• Ryazanov AG, Pavur KS, Dorovkov MV
• Alpha-kinases: a new class of protein kinases with a novel catalytic domain.
• Curr Biol. 1999; 9: 435-435

• Stewart AE, Dowd S, Keyse SM, McDonald NQ
• Crystal structure of the MAPK phosphatase Pyst1 catalytic domain and implications for regulated activation.
• Nat Struct Biol. 1999; 6: 174-81
• Display abstract

• The crystal structure of the catalytic domain from the MAPK phosphatase Pyst1 (Pyst1-CD) has been determined at 2.35 A. The structure adopts a protein tyrosine phosphatase (PTPase) fold with a shallow active site that displays a distorted geometry in the absence of its substrate with some similarity to the dual-specificity phosphatase cdc25. Functional characterization of Pyst1-CD indicates it is sufficient to dephosphorylate activated ERK2 in vitro. Kinetic analysis of Pyst1 and Pyst1-CD using the substrate p-nitrophenyl phosphate (pNPP) reveals that both molecules undergo catalytic activation in the presence of recombinant inactive ERK2, switching from a low- to high-activity form. Mutation of Asp 262, located 5.5 A distal to the active site, demonstrates it is essential for catalysis in the high-activity ERK2-dependent conformation of Pyst1 but not for the low-activity ERK2-independent form, suggesting that ERK2 induces closure of the Asp 262 loop over the active site, thereby enhancing Pyst1 catalytic efficiency.

• Harris KF, Shoji I, Cooper EM, Kumar S, Oda H, Howley PM
• Ubiquitin-mediated degradation of active Src tyrosine kinase.
• Proc Natl Acad Sci U S A. 1999; 96: 13738-43
• Display abstract

• Src family tyrosine kinases are involved in modulating various signal transduction pathways leading to the induction of DNA synthesis and cytoskeletal reorganization in response to cell-cell or cell-matrix adhesion. The critical role of these kinases in regulating cellular signaling pathways requires that their activity be tightly controlled. Src family proteins are regulated through reversible phosphorylation and dephosphorylation events that alter the conformation of the kinase. We have found evidence that Src also is regulated by ubiquitination. Activated forms of Src are less stable than either wild-type or kinase-inactive Src mutants and can be stabilized by proteasome inhibitors. In addition, poly-ubiquitinated forms of active Src have been detected in vivo. Taken together, our results establish ubiquitin-mediated proteolysis as a previously unidentified mechanism for irreversibly attenuating the effects of active Src kinase.

• Stenberg KA, Riikonen PT, Vihinen M
• KinMutBase, a database of human disease-causing protein kinase mutations.
• Nucleic Acids Res. 1999; 27: 362-4
• Display abstract

• KinMutBase (http://www.uta.fi/laitokset/imt/KinMut Base.html) is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signalling molecules, in which mutations can lead into diseases including, e.g., immunodeficiencies, cancers and endocrine disorders. The first release of KinMutBase contains information for nine protein tyrosine kinases. There are altogether 170 entries representing 273 families and 403 patients. Mutations appear both in conserved hallmark residues of the kinases as well as in non-homologous sites. The KinMutBase WWW pages provide plenty of information, namely mutation statistics and display, clickable sequences with mutations, restriction enzyme patterns and online submission.

• Dong B, Silverman RH
• Alternative function of a protein kinase homology domain in 2', 5'-oligoadenylate dependent RNase L.
• Nucleic Acids Res. 1999; 27: 439-45
• Display abstract

• RNase L is the 2',5'-oligoadenylate (2-5A)-dependent endoribonuclease that functions in interferon action and apoptosis. One of the intriguing, albeit unexplained, features of RNase L is its significant homology to protein kinases. Despite the homology, however, no protein kinase activity was detected during activation and RNA cleavage reactions with human RNase L. Similarly, the kinase plus ribonuclease domains of RNase L produced no detectable protein kinase activity in contrast to the phosphorylation obtained with homologous domains of the related kinase and endoribonuclease, yeast IRE1p. In addition, neither ATP nor pA(2'p5'A)3was hydrolyzed by RNase L. To further investigate the function of the kinase homology in RNase L, the conserved lysine at residue 392 in protein kinase-like domain II was replaced with an arginine residue. The resulting mutant, RNase LK392R, showed >100-fold decreases in 2-5A-dependent ribonuclease activity without reducing 2-5A- or RNA-binding activities. The greatly reduced activity of RNase LK392Rwas correlated to a defect in the ability of RNase L to dimerize. These results demonstrate a critical role for lysine 392 in the activation and dimerization of RNase L, thus suggesting that these two activities are intimately linked.

• Kameshita I, Taketani S, Ishida A, Fujisawa H
• Detection of a variety of Ser/Thr protein kinases using a synthetic peptide with multiple phosphorylation sites.
• J Biochem (Tokyo). 1999; 126: 991-5
• Display abstract

• A novel peptide with multiple phosphorylation sites, which we designated as multide, was developed to detect a wide variety of protein kinases in crude cell extracts. Multide, KKRKSSLRRWSPLTPRQMSFDC, has been designed to contain consensus sequences for various Ser/Thr protein kinases including cAMP-dependent protein kinase, protein kinase C, MAP kinases, and Ca(2+)/calmodulin-dependent protein kinases in a single peptide. In-gel protein kinase assay using multide was found to be very useful for analyzing the activities of protein kinases that are altered in response to various extracellular stimuli. The substrate specificities of the protein kinases thus detected were further determined by using five multide analogs with different phosphorylation sites.

• Gross SD, Anderson RA
• Casein kinase I: spatial organization and positioning of a multifunctional protein kinase family.
• Cell Signal. 1998; 10: 699-711
• Display abstract

• The casein kinase I family of serine/threonine protein kinases is highly conserved from yeast to humans. Until only recently, both the function and regulation of these enzymes remained poorly uncharacterised in that they appeared to be constitutively active and were capable of phosphorylating an untold number of other proteins. While relatively little was known regarding the exact function of the higher eukaryotic isoforms, the casein kinase I (CKI) isoforms from yeast have been genetically linked to vesicular trafficking, DNA repair, cell cycle progression and cytokinesis. All five S. cerevisiae isoforms are known to be associated with discrete cellular compartments and this localization has been shown to be absolutely essential for their respective functions. New evidence now suggests that the CKI isoforms in more complex systems also exhibit non-homogeneous subcellular distributions that may prove vital to defining the function and regulation of these enzymes. In particular, CKIalpha, the most-characterized vertebrate isoform, is associated with cytosolic vesicles, the mitotic spindle and structures within the nucleus. Functions associated with these localizations coincide with those previously reported in yeast, suggesting a conservation of function. Other reports have indicated that each of the remaining CKI isoforms have the capacity to make associations with components of several signal transduction pathways, thereby channeling CKI function toward specific regulatory events. This review will examine what is now known about the higher eukaryotic CKI family members from the perspective localization as a means of gaining a better understanding of the function and regulation of these kinases.

• Mayans O et al.
• Structural basis for activation of the titin kinase domain during myofibrillogenesis.
• Nature. 1998; 395: 863-9
• Display abstract

• The giant muscle protein titin (connectin) is essential in the temporal and spatial control of the assembly of the highly ordered sarcomeres (contractile units) of striated muscle. Here we present the crystal structure of titin's only catalytic domain, an autoregulated serine kinase (titin kinase). The structure shows how the active site is inhibited by a tyrosine of the kinase domain. We describe a dual mechanism of activation of titin kinase that consists of phosphorylation of this tyrosine and binding of calcium/calmodulin to the regulatory tail. The serine kinase domain of titin is the first known non-arginine-aspartate kinase to be activated by phosphorylation. The phosphorylated tyrosine is not located in the activation segment, as in other kinases, but in the P + 1 loop, indicating that this tyrosine is a binding partner of the titin kinase substrate. Titin kinase phosphorylates the muscle protein telethonin in early differentiating myocytes, indicating that this kinase may act in myofibrillogenesis.

• Marino-Buslje C, Mizuguchi K, Siddle K, Blundell TL
• A third fibronectin type III domain in the extracellular region of the insulin receptor family.
• FEBS Lett. 1998; 441: 331-6
• Display abstract

• The insulin receptor family consists of the homologous tyrosine kinase receptors, insulin receptor (IR), insulin-like growth factor 1 receptor (IGF1R) and insulin receptor-related receptor. The three-dimensional structures of the tyrosine kinase domain of the IR and the first three extracellular domains (L1, Cys-rich and L2) of the IGF1R are known. Here we present evidence that the connecting domain of the IR family is a member of the fibronectin type II (FnIII) superfamily. Structure-based alignment of FnIII domains reveals several key residues that are also conserved in the sequence of the connecting domain. The alignment of the connecting domain with FnIII domains is in good agreement with secondary structure prediction. A model of the connecting domain shows a hydrophobic core formed by the conserved residues and is consistent with previously known biochemical data. This suggests that the IR family contains three FnIII domains in tandem in the extracellular juxtamembrane region.

• Scott JD, Faux MC
• Use of synthetic peptides in the dissection of protein-targeting interactions.
• Methods Mol Biol. 1998; 88: 161-85

• Tanaka T et al.
• NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ.
• Nature. 1998; 396: 88-92
• Display abstract

• Bacteria live in capricious environments, in which they must continuously sense external conditions in order to adjust their shape, motility and physiology. The histidine-aspartate phosphorelay signal-transduction system (also known as the two-component system) is important in cellular adaptation to environmental changes in both prokaryotes and lower eukaryotes. In this system, protein histidine kinases function as sensors and signal transducers. The Escherichia coli osmosensor, EnvZ, is a transmembrane protein with histidine kinase activity in its cytoplasmic region. The cytoplasmic region contains two functional domains: domain A (residues 223-289) contains the conserved histidine residue (H243), a site of autophosphorylation as well as transphosphorylation to the conserved D55 residue of response regulator OmpR, whereas domain B (residues 290-450) encloses several highly conserved regions (G1, G2, F and N boxes) and is able to phosphorylate H243. Here we present the solution structure of domain B, the catalytic core of EnvZ. This core has a novel protein kinase structure, distinct from the serine/threonine/tyrosine kinase fold, with unanticipated similarities to both heatshock protein 90 and DNA gyrase B.

• Hutchison M, Berman KS, Cobb MH
• Isolation of TAO1, a protein kinase that activates MEKs in stress-activated protein kinase cascades.
• J Biol Chem. 1998; 273: 28625-32
• Display abstract

• Several components of the budding yeast pheromone-response pathway are conserved in mammalian mitogen-activated protein (MAP) kinase pathways. Thus, we used degenerate oligonucleotides derived from the sequence of the Saccharomyces cerevisiae protein kinase Ste20p to amplify related sequences from the rat. One of these sequences was used to clone a rat Ste20p homolog, which we called TAO1 for its one thousand and one amino acids. Northern analysis shows TAO1 is highly expressed in brain, as is a homolog TAO2. Recombinant TAO1 was expressed and purified from Sf9 cells. In vitro, it activated MAP/extracellular signal-regulated protein kinase (ERK) kinases (MEKs) 3, 4, and 6 of the stress-responsive MAP kinase pathways, but not MEK1 or 2 of the classical MAP kinase pathway. TAO1 activated MEK3 but not MEK4 or MEK6 in transfected cells. MEK3 coimmunoprecipitated with TAO1 when they were expressed in 293 cells. In addition, immunoreactive MEK3 endogenous to Sf9 cells copurified with TAO1 produced from a recombinant baculovirus. The activation of and binding to MEK3 by TAO1 implicates TAO1 in the regulation of the p38-containing stress-responsive MAP kinase pathway.

• Briozzo P et al.
• Structures of escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity.
• Structure. 1998; 6: 1517-27
• Display abstract

• Background:. Nucleoside monophosphate kinases (NMP kinases) catalyze the reversible transfer of a phosphoryl group from a nucleoside triphosphate to a nucleoside monophosphate. Among them, cytidine monophosphate kinase from Escherichia coli has a striking particularity: it is specific for CMP, whereas in eukaryotes a unique UMP/CMP kinase phosphorylates both CMP and UMP with similar efficiency. Results:. The crystal structure of the CMP kinase apoenzyme from E. coli was solved by single isomorphous replacement and refined at 1.75 A resolution. The structure of the enzyme in complex with CDP was determined at 2.0 A resolution. Like other NMP kinases, the protein contains a central parallel beta sheet, the strands of which are connected by alpha helices. The enzyme differs from other NMP kinases in the presence of a 40-residue insert situated in the NMP-binding (NMPbind) domain. This insert contains two domains: one comprising a three-stranded antiparallel beta sheet, the other comprising two alpha helices. Conclusions:. Two features of the CMP kinase from E. coli have no equivalent in other NMP kinases of known structure. Firstly, the large NMPbind insert undergoes a CDP-induced rearrangement: its beta-sheet domain moves away from the substrate, whereas its helical domain comes closer to it in a motion likely to improve the protection of the active site. Secondly, residues involved in CDP recognition are conserved in CMP kinases and have no counterpart in other NMP kinases. The structures presented here are the first of a new family of NMP kinases specific for CMP.

• Donella-Deana A, Cesaro L, Ruzzene M, Brunati AM, Marin O, Pinna LA
• Spontaneous autophosphorylation of Lyn tyrosine kinase at both its activation segment and C-terminal tail confers altered substrate specificity.
• Biochemistry. 1998; 37: 1438-46
• Display abstract

• Two tyrosyl residues have been reported to play a crucial role in the regulation of protein tyrosine kinases of the Src family: autophosphorylation of Tyr416 (c-Src numbering) located in the catalytic domain correlates with enzyme activation, while Csk-mediated phosphorylation of the C-terminal tyrosine Tyr527 (c-Src numbering) gives rise to inactive forms of Src kinases. Here we show that the Src-related Lyn kinase undergoes spontaneous and stoichiometric autophosphorylation at both Tyr396 (homologous to c-Src Tyr416) and Tyr507 (homologous to c-Src Tyr527). Such a doubly autophosphorylated form of Lyn is hyperactive toward peptide substrates and insensitive to Csk-induced downregulation. In contrast, doubly autophosphorylated Lyn exhibits reduced activity toward protein substrates such as phospho-p50/HS1 (hematopoietic-lineage cell-specific protein) and p57/PDI (protein disulfide isomerase related protein), whose multiple sequential/processive phosphorylation relies on the accessibility of the SH2 domain of the kinase. These data disclose a novel conformation of Lyn that is catalytically active despite the presence of an intramolecular interaction between the phosphorylated tail and the SH2 domain. This enzyme conformation is expected to display a reduced oncogenic potential resulting from its defective recognition of a subset of protein substrates whose targeting is mediated by the Lyn SH2 domain.

• Gehrmann T, Heilmeyer LM Jr
• Phosphatidylinositol 4-kinases.
• Eur J Biochem. 1998; 253: 357-70
• Display abstract

• Polyphosphoinositides are involved in many signal transduction pathways in eukaryotic cells. The first committed step is catalysed by phosphatidylinositol 4-kinase leading to the formation of phosphatidylinositol 4-phosphate. In the last four years, ten cDNA molecules have been cloned which code isoforms of phosphatidylinositol 4-kinase; some of which are highly related. Characteristically, they contain a C-terminal catalytic domain which is similar to that of (poly)phosphoinositide 3-kinases and to that of more distantly related lipid/protein kinases. Alignment has characterised cDNAs from Chaenorabditis, Dictyostelium and Schizostaphyloccus pombe as those of phosphatidylinositol 4-kinases also. All these lipid kinases are related to the superfamily of protein kinases. Several amino acids are highly conserved in catalytic domains of lipid and protein kinases. Employing the catalytic subunit of the cAMP-dependent protein kinase as template, these residues can be assigned functionally. On the basis of the alignment, a phylogenetic tree of the superfamily of phosphatidylinositol kinases has been constructed. Three families, the phosphatidylinositol 4-kinases, phosphoinositide 3-kinases, and the phosphatidylinositol related lipid/protein kinases, can be recognised. Each family comprises two subfamilies. The involvement of the phosphatidylinositol 4-kinases in signal transduction processes is summarised and a new hypothesis for the function of their isoforms in polyphosphoinositide signalling is presented. The involvement of phosphatidylinositol 4-kinases in formation of lipid-protein interactions with cytoskeleton proteins and the metabolism of polyphosphoinositide in the nucleus is discussed.

• Himanen JP, Henkemeyer M, Nikolov DB
• Crystal structure of the ligand-binding domain of the receptor tyrosine kinase EphB2.
• Nature. 1998; 396: 486-91
• Display abstract

• The Eph receptors, which bind a group of cell-membrane-anchored ligands known as ephrins, represent the largest subfamily of receptor tyrosine kinases (RTKs). They are predominantly expressed in the developing and adult nervous system and are important in contact-mediated axon guidance, axon fasciculation and cell migration. Eph receptors are unique among other RTKs in that they fall into two subclasses with distinct ligand specificities, and in that they can themselves function as ligands to activate bidirectional cell-cell signalling. We report here the crystal structure at 2.9 A resolution of the amino-terminal ligand-binding domain of the EphB2 receptor (also known as Nuk). The domain folds into a compact jellyroll beta-sandwich composed of 11 antiparallel beta-strands. Using structure-based mutagenesis, we have identified an extended loop that is important for ligand binding and class specificity. This loop, which is conserved within but not between Eph RTK subclasses, packs against the concave beta-sandwich surface near positions at which missense mutations cause signalling defects, localizing the ligand-binding region on the surface of the receptor.

• Niefind K, Guerra B, Pinna LA, Issinger OG, Schomburg D
• Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution.
• EMBO J. 1998; 17: 2451-62
• Display abstract

• CK2alpha is the catalytic subunit of protein kinase CK2, an acidophilic and constitutively active eukaryotic Ser/Thr kinase involved in cell proliferation. A crystal structure, at 2.1 A resolution, of recombinant maize CK2alpha (rmCK2alpha) in the presence of ATP and Mg2+, shows the enzyme in an active conformation stabilized by interactions of the N-terminal region with the activation segment and with a cluster of basic residues known as the substrate recognition site. The close interaction between the N-terminal region and the activation segment is unique among known protein kinase structures and probably contributes to the constitutively active nature of CK2. The active centre is occupied by a partially disordered ATP molecule with the adenine base attached to a novel binding site of low specificity. This finding explains the observation that CK2, unlike other protein kinases, can use both ATP and GTP as phosphorylating agents.

• Lawrie AM, Noble ME, Tunnah P, Brown NR, Johnson LN, Endicott JA
• Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2.
• Nat Struct Biol. 1997; 4: 796-801
• Display abstract

• Staurosporine exhibits nanomolar IC50 values against a wide range of protein kinases. The structure of a CDK2 staurosporine complex explains the tight binding of this inhibitor, and suggests features to be exploited in the design of specific inhibitors of CDKs.

• Andersen G et al.
• The structure of cyclin H: common mode of kinase activation and specific features.
• EMBO J. 1997; 16: 958-67
• Display abstract

• The crystal structure of human cyclin H refined at 2.6 A resolution is compared with that of cyclin A. The core of the molecule consists of two repeats containing five helices each and forming the canonical cyclin fold also observed in TFIIB. One hundred and thirty-two out of the 217 C alpha atoms from the cyclin fold can be superposed with a root-mean-square difference of 1.8 A. The structural homology is even higher for the residues at the interface with the kinase, which is of functional significance, as shown by our observation that cyclin H binds to cyclin-dependent kinase 2 (cdk2) and that cyclin A is able to activate cdk7 in the presence of MAT1. Based on this superposition, a new signature sequence for cyclins was found. The specificity of the cyclin H molecule is provided mainly by two long helices which extend the cyclin fold at its N- and C-termini and pack together against the first repeat on the side opposite to the kinase. Deletion mutants show that the terminal helices are required for a functionally active cyclin H.

• Nishihama R, Banno H, Kawahara E, Irie K, Machida Y
• Possible involvement of differential splicing in regulation of the activity of Arabidopsis ANP1 that is related to mitogen-activated protein kinase kinase kinases (MAPKKKs).
• Plant J. 1997; 12: 39-48
• Display abstract

• Three types of Arabidopsis cDNA (cANP1, cANP2 and cANP3) have been isolated that encode putative protein kinases, designated ANP1, ANP2 and ANP3. These kinases exhibit a high degree of homology to NPK1, a tobacco protein that is a member of the family of mitogen-activated protein kinase kinase kinases (MAPKKKs), which appears to function in the proliferation of tobacco cells. The predicted amino acid sequences of the kinase domains in the amino-terminal halves of the ANPs were more than 80% identical to that of NPK1, while the kinase-unrelated regions in the carboxy-terminal halves exhibited relatively low homology. Two species of cANP1 were identified, ANP1L cDNA (cANP1L) and ANP1S cDNA (cANP1S), which were derived from a single ANP1 gene: the former had an intron-like sequence in the coding region for the kinase-unrelated region, while the latter did not include such an intron-like sequence. cANP1L encoded a putative protein with both kinase and kinase-unrelated domains, resembling NPK1, whereas cANP1S encoded only the amino-terminal kinase domain because the intron-like sequence was absent, with resulting elimination of most of the kinase-unrelated region. Genetic analysis with mutant yeast cells showed that over-expression of cANP1L or of cANP1S activated the mating pheromone-responsive signal pathway which is mediated by a MAP kinase cascade. Moreover, the extent of such activation by cANP1S was greater than that by cANP1L. These results predict that differential splicing of the intron-like sequence in the ANP1 transcript might be at least one of the molecular mechanisms involved in the generation of active ANP1 protein kinase.

• Hubbard SR
• Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog.
• EMBO J. 1997; 16: 5572-81
• Display abstract

• The crystal structure of the phosphorylated, activated form of the insulin receptor tyrosine kinase in complex with a peptide substrate and an ATP analog has been determined at 1.9 A resolution. The activation loop (A-loop) of the kinase undergoes a major conformational change upon autophosphorylation of Tyr1158, Tyr1162 and Tyr1163 within the loop, resulting in unrestricted access of ATP and protein substrates to the kinase active site. Phosphorylated Tyr1163 (pTyr1163) is the key phosphotyrosine in stabilizing the conformation of the tris-phosphorylated A-loop, whereas pTyr1158 is completely solvent-exposed, suggesting an availability for interaction with downstream signaling proteins. The YMXM-containing peptide substrate binds as a short anti-parallel beta-strand to the C-terminal end of the A-loop, with the methionine side chains occupying two hydrophobic pockets on the C-terminal lobe of the kinase. The structure thus reveals the molecular basis for insulin receptor activation via autophosphorylation, and provides insights into tyrosine kinase substrate specificity and the mechanism of phosphotransfer.

• Lamparter T, Mittmann F, Gartner W, Borner T, Hartmann E, Hughes J
• Characterization of recombinant phytochrome from the cyanobacterium Synechocystis.
• Proc Natl Acad Sci U S A. 1997; 94: 11792-7
• Display abstract

• The complete sequence of the Synechocystis chromosome has revealed a phytochrome-like sequence that yielded an authentic phytochrome when overexpressed in Escherichia coli. In this paper we describe this recombinant Synechocystis phytochrome in more detail. Islands of strong similarity to plant phytochromes were found throughout the cyanobacterial sequence whereas C-terminal homologies identify it as a likely sensory histidine kinase, a family to which plant phytochromes are related. An approximately 300 residue portion that is important for plant phytochrome function is missing from the Synechocystis sequence, immediately in front of the putative kinase region. The recombinant apoprotein is soluble and can easily be purified to homogeneity by affinity chromatography. Phycocyanobilin and similar tetrapyrroles are covalently attached within seconds, an autocatalytic process followed by slow conformational changes culminating in red-absorbing phytochrome formation. Spectral absorbance characteristics are remarkably similar to those of plant phytochromes, although the conformation of the chromophore is likely to be more helical in the Synechocystis phytochrome. According to size-exclusion chromatography the native recombinant apoproteins and holoproteins elute predominantly as 115- and 170-kDa species, respectively. Both tend to form dimers in vitro and aggregate under low salt conditions. Nevertheless, the purity and solubility of the recombinant gene product make it a most attractive model for molecular studies of phytochrome, including x-ray crystallography.

• Wilson KP et al.
• Crystal structure of p38 mitogen-activated protein kinase.
• J Biol Chem. 1996; 271: 27696-700
• Display abstract

• p38 mitogen-activated protein kinase is activated by environmental stress and cytokines and plays a role in transcriptional regulation and inflammatory responses. The crystal structure of the apo, unphosphorylated form of p38 kinase has been solved at 2.3 A resolution. The fold and topology of p38 is similar to ERK2 (Zhang, F., Strand, A., Robbins, D., Cobb, M. H., and Goldsmith, E. J. (1994) Nature 367, 704-711). The relative orientation of the two domains of p38 kinase is different from that observed in the active form of cAMP-dependent protein kinase. The twist results in a misalignment of the active site of p38, suggesting that the orientation of the domains would have to change before catalysis could proceed. The residues that are phosphorylated upon activation of p38 are located on a surface loop that occupies the peptide binding channel. Occlusion of the active site by the loop, and misalignment of catalytic residues, may account for the low enzymatic activity of unphosphorylated p38 kinase.

• Ruzzene M, Brunati AM, Marin O, Donella-Deana A, Pinna LA
• SH2 domains mediate the sequential phosphorylation of HS1 protein by p72syk and Src-related protein tyrosine kinases.
• Biochemistry. 1996; 35: 5327-32
• Display abstract

• The protein tyrosine kinase p72syk readily phosphorylates hematopoietic linkage cell-specific protein p50/HS1 with high stoichiometry (up to 4 mol of Pi/mol of protein) and favorable kinetic constants (Km 77 nM, kcat 0.37 s-1), at sites that display the motif that is specifically recognized by the HS2 domains of Src tyrosine kinases. Such a phosphorylation converts p50/HS1 into a good substrate for c-Fgr, which in contrast is nearly inactive on nonphosphorylated p50/HS1. A phosphopeptide reproducing one of the main p50/HS1 site affected by p72syk, but neither its dephosphorylated derivative nor other phosphopeptides with different structure, blocks the secondary phosphorylation of phospho(p50/HS1) by c-Fgr but not its primary phosphorylation by p72syk. It also prevents the coimmunoprecipitation of phospho(HS1) with c-Fgr by anti-(c-Fgr) antibodies. In contrast the HS1[393-402] phosphopeptide is ineffective on the kinase activity of c-Fgr when tested with peptide substrates, showing that inhibition of p50/HS1 phosphorylation is not exerted at the catalytic site of c-Fgr. The sequential phosphorylation of p50/HS1 as well as its specific blockage by the HS1 phosphopeptide is also observable if c-Fgr is replaced by two other Src-related kinases, namely, Lyn and Fyn, as secondary phosphorylating agents. None of these Src-related kinases, however, can carry out the phosphorylation of p50/HS1 at the sites affected by p72syk, even after prolonged incubation. Our data suggest that sequential phosphorylation might represent a general mechanism by which p72syk and other Syk-related kinases generate substrates for Src-related protein tyrosine kinases. They also show that sequential phosphorylation (requiring the concerted action of a primary and a secondary kinases) cannot be surrogated by "processive" phosphorylation where a single kinase catalyzes both the primary and secondary phosphorylation, although both these modes of multiple phosphorylation are based on interactions between SH2 domains of the kinases and phosphotyrosyl sites of the substrate.

• Li S, Wilson ME, Donelson JE
• Leishmania chagasi: a gene encoding a protein kinase with a catalytic domain structurally related to MAP kinase kinase.
• Exp Parasitol. 1996; 82: 87-96
• Display abstract

• The gene for a serine/threonine protein kinase was isolated from Leishmania chagasi. The deduced amino acid sequence encoded by this Leishmania protein kinase (LPK-1) gene possesses all of the 11 conserved subdomains found in most other serine/threonine protein kinase catalytic domains. Sequence alignment with other known protein kinases demonstrates that the 42-kDa LPK-1 is a member of the mitogen-activated protein kinase kinase family involved in the signal-transduction pathways in yeast and mammalian cells. The single copy gene for LPK-1 specifies a 3.1-kb mRNA that is expressed in both logarithmic and stationary phase promastigotes with a twofold higher steady-state level in the infective stationary phase promastigotes.

• Kobe B et al.
• Giant protein kinases: domain interactions and structural basis of autoregulation.
• EMBO J. 1996; 15: 6810-21
• Display abstract

• The myosin-associated giant protein kinases twitchin and titin are composed predominantly of fibronectin- and immunoglobulin-like modules. We report the crystal structures of two autoinhibited twitchin kinase fragments, one from Aplysia and a larger fragment from Caenorhabditis elegans containing an additional C-terminal immunoglobulin-like domain. The structure of the longer fragment shows that the immunoglobulin domain contacts the protein kinase domain on the opposite side from the catalytic cleft, laterally exposing potential myosin binding residues. Together, the structures reveal the cooperative interactions between the autoregulatory region and the residues from the catalytic domain involved in protein substrate binding, ATP binding, catalysis and the activation loop, and explain the differences between the observed autoinhibitory mechanism and the one found in the structure of calmodulin-dependent kinase I.

• Johnson LN, Noble ME, Owen DJ
• Active and inactive protein kinases: structural basis for regulation.
• Cell. 1996; 85: 149-58

• Adler K, Gerisch G, von Hugo U, Lupas A, Schweiger A
• Classification of tyrosine kinases from Dictyostelium discoideum with two distinct, complete or incomplete catalytic domains.
• FEBS Lett. 1996; 395: 286-92
• Display abstract

• Two new kinases of Dictyostelium discoideum were identified by screening of a (lambda)gt11 expression library with a phosphotyrosine specific antibody. Amino-acid sequences derived from cDNA and genomic clones indicate that DPYK3 is a protein of 150 kDa and DPYK4, a protein of 75 kDa. The C-terminal fragments of each protein were produced in Escherichia coli and shown to be autocatalytically phosphorylated at tyrosine residues. A common feature of these kinases is the presence of two different sequence stretches in tandem that are related to kinase catalytic domains. The sequence relationships of DPYK3 and 4 to other protein kinases, and the positions of their catalytic domain sequences within the phylogenetic tree of protein kinases were analysed. Domains I of both kinases and domain II of DPYK3 constitute, together with the catalytic domains of two previously described tyrosine kinases of D. discoideum, a branch of their own, separate from the tyrosine kinase domains in sensu strictu. Domain II in DPYK4 is found on a different branch close to serine/threonine kinases.

• Chow LM, Veillette A
• The Src and Csk families of tyrosine protein kinases in hemopoietic cells.
• Semin Immunol. 1995; 7: 207-26
• Display abstract

• There is increasing evidence that the Src family of cytoplasmic tyrosine protein kinases is involved in the signal transduction of antigen receptor- and Fc receptor-mediated cellular activation. This function relates at least in part to the ability of Src-related enzymes to phosphorylate conserved tyrosine-based motifs in the cytoplasmic domains of the antigen and Fc receptors. The catalytic function of Src-like products is repressed by phosphorylation of a conserved carboxy-terminal tyrosine residue, which is mediated by another cellular tyrosine protein kinase, p50csk. Based on this property, it is postulated that Csk is a potent negative regulator of antigen and Fc receptor signalling. The balance between the actions of Src-related kinases and the p50csk is likely a major determinant of immune responsiveness.

• Benner SA
• Predicting the conformation of proteins from sequences. Progress and future progress.
• J Mol Recognit. 1995; 8: 9-28
• Display abstract

• Recent progress in structure prediction has allowed bona fide predictions, those made and published before an experimental structure is determined, to be remarkably accurate. The most successful methods rely on an analysis of patterns of conservation and variation within homologous protein sequences, extract tertiary structural information before secondary structure is predicted, and avoid 'three state per residue scores' as a tool for evaluating a prediction, focusing instead on efforts to understand why a prediction is successful when it is successful, and why it fails when it fails.

• Kuma K, Iwabe N, Miyata T
• Functional constraints against variations on molecules from the tissue level: slowly evolving brain-specific genes demonstrated by protein kinase and immunoglobulin supergene families.
• Mol Biol Evol. 1995; 12: 123-30
• Display abstract

• In the protein kinase family, the basic function of kinase domain is similar among members. According to the standard view of functional constraint, the molecular evolutionary rate depends on functional and structural features characteristic of individual molecules (local constraint). Thus the evolutionary rate of the kinase domain is expected to be similar for different members. Contrary to this expectation, a comparison of the evolutionary rates revealed a wide difference among members; it amounts to about 100 times difference between the maximum and minimum rates. A similar result was also found in members of the immunoglobulin (Ig) family. In addition, significant correlations in evolutionary rate were observed between the kinase domain and the Ig-like domain in the receptor protein tyrosine kinases and between the kinase domain and the SH domain in the nonreceptor-type kinases. Furthermore, the evolutionary rates of family members that are expressed tissue specifically differ widely, depending on their tissue distribution: members expressed in the brain evolve with significantly slower rates than those expressed in the immune system. These results strongly suggest the presence of an alternative constraint (global constraint) against changes on molecules derived from higher levels like tissues or organs.

• Toomey CM, Flinn N, van der Walle C, Toth I, Munday MR
• Peptide substrates for AMP-activated protein kinase.
• Biochem Soc Trans. 1995; 23: 141-141

• Shibata W et al.
• A tobacco protein kinase, NPK2, has a domain homologous to a domain found in activators of mitogen-activated protein kinases (MAPKKs).
• Mol Gen Genet. 1995; 246: 401-10
• Display abstract

• A cDNA (cNPK2) that encodes a protein of 518 amino acids was isolated from a library prepared from poly(A)+ RNAs of tobacco cells in suspension culture. The N-terminal half of the predicted NPK2 protein is similar in amino acid sequence to the catalytic domains of kinases that activate mitogen-activated protein kinases (designated here MAPKKs) from various animals and to those of yeast homologs of MAPKKs. The N-terminal domain of NPK2 was produced as a fusion protein in Escherichia coli, and the purified fusion protein was found to be capable of autophosphorylation of threonine and serine residues. These results indicate that the N-terminal domain of NPK2 has activity of a serine/threonine protein kinase. Southern blot analysis showed that genomic DNAs from various plant species, including Arabidopsis thaliana and sweet potato, hybridized strongly with cNPK2, indicating that these plants also have genes that are closely related to the gene for NPK2. The structural similarity between the catalytic domain of NPK2 and those of MAPKKs and their homologs suggests that tobacco NPK2 corresponds to MAPKKs of other organisms. Given the existence of plant homologs of an MAP kinase and tobacco NPK1, which is structurally and functionally homologous to one of the activator kinases of yeast homologs of MAPKK (MAPKKKs), it seems likely that a signal transduction pathway mediated by a protein kinase cascade that is analogous to the MAP kinase cascades proposed in yeasts and animals, is also conserved in plants.

• Hind G, Marshak DR, Coughlan SJ
• Spinach thylakoid polyphenol oxidase: cloning, characterization, and relation to a putative protein kinase.
• Biochemistry. 1995; 34: 8157-64
• Display abstract

• A 64-kDa protein was purified from an octyl glucoside/cholate extract of spinach thylakoids. N-Terminal analysis yielded 23 residues of sequence, of which the first 15 were identical to a sequence reported [Gal, A., Herrmann, R. G., Lottspeich, F., & Ohad, I. (1992) FEBS Lett. 298, 33-35] for a protein kinase with specificity toward the photosystem II light-harvesting complex (LHC-II). We report the complete sequence of this 64-kDa protein, deduced from cDNA clones. The transit peptide has a chloroplast import signal at the N-terminus and a C-terminal hydrophobic span bounded by basic amino acids that predicts localization of the protein to the thylakoid lumen. The mature protein sequence is about 50% identical to several polyphenol oxidases (PPOs). Canonical protein kinase motifs are absent, as are sequences characteristic of ATP-binding sites. The mature protein resembles arthropodan hemocyanin (Hc), possessing three major domains. The N-terminal domain is rich in cysteine residues and predicted alpha-helices. The central domain has a conserved motif, N-terminal to a presumptive Cu-A site, that is not found in tyrosinases or Hc and is proposed as the provider of a third imidazole ligand to Cu-A. An unusual 13-residue, glutamine-rich link begins a C-terminal domain containing 7 predicted beta-strands which, by analogy with Hc, may form an antiparallel beta-barrel. We conclude that this 64-kDa polypeptide is a lumenal PPO and the precursor of a 42.5-kDa PPO form described previously [Golbeck, J. H., & Cammarata, K. V. (1981) Plant Physiol. 67, 977-984].(ABSTRACT TRUNCATED AT 250 WORDS)

• McDonald NQ, Murray-Rust J, Blundell TL
• The first structure of a receptor tyrosine kinase domain: a further step in understanding the molecular basis of insulin action.
• Structure. 1995; 3: 1-6
• Display abstract

• Both the observed cis-inhibition and the proposed trans-activation of the insulin receptor tyrosine kinase help explain insulin signalling through its receptor.

• Stone JM, Walker JC
• Plant protein kinase families and signal transduction.
• Plant Physiol. 1995; 108: 451-7
• Display abstract

• Enzymes of the eukaryotic protein kinase superfamily catalyze the reversible transfer of the gamma-phosphate from ATP to amino acid side chains of proteins. Protein kinase function can be counteracted by the action of phosphoprotein phosphatases. Phosphorylation status of a protein can have profound effects on its activity and interaction with other proteins. An estimated 1 to 3% of functional eukaryotic genes encode protein kinases, suggesting that they are involved in many aspects of cellular regulation and metabolism. In plants, protein phosphorylation has been implicated in responses to many signals, including light, pathogen invasion, hormones, temperature stress, and nutrient deprivation. Activities of several plant metabolic and regulatory enzymes are also controlled by reversible phosphorylation. As might be expected from this diversity of function, there is a large array of different protein kinases. Purification of protein kinases and their subsequent cloning, facilitated by the PCR and advances in homology-based cloning techniques, as well as functional analyses, including complementation of conditional yeast mutants and positional cloning of mutant plant genes, has already led to identification of more than 70 plant protein kinase genes. However, the precise functional roles of specific protein kinases and phosphatases during plant growth and development have been elucidated for only a few.

• Xu RM, Carmel G, Sweet RM, Kuret J, Cheng X
• Crystal structure of casein kinase-1, a phosphate-directed protein kinase.
• EMBO J. 1995; 14: 1015-23
• Display abstract

• The structure of a truncated variant of casein kinase-1 from Schizosaccharomyces pombe, has been determined in complex with MgATP at 2.0 A resolution. The model resembles the 'closed', ATP-bound conformations of the cyclin-dependent kinase 2 and the cAMP-dependent protein kinase, with clear differences in the structure of surface loops that impart unique features to casein kinase-1. The structure is of unphosphorylated, active conformation of casein kinase-1 and the peptide-binding site is fully accessible to substrate.

• Smith RF, King KY
• Identification of a eukaryotic-like protein kinase gene in Archaebacteria.
• Protein Sci. 1995; 4: 126-9
• Display abstract

• Primary sequence patterns based on known conserved sites in eukaryotic protein kinases were used to search for eukaryotic-like protein kinase sequences in a six-frame translation of the bacterial subsection of GenBank. This search identified a previously unrecognized eukaryotic-like protein kinase gene in three related methanogenic archaebacteria, Methanococcus vannielii, M. voltae, and M. thermolithotrophicus. The proposed coding sequences are located in orthologous open reading frames (ORFs): ORF547, ORF294, and ORF114, respectively. The C-terminus of the ORFs contains 9 of the 11 subdomains characteristically conserved within the eukaryotic protein kinase catalytic domain. The N-terminus of the ORFs is similar to a putative glycoprotease in Pasteurella haemolytica and its homologue in Escherichia coli, the orfX gene. This is the first report of a eukaryotic-like protein kinase sequence observed in Archaebacteria.

• Yang SD, Huang TJ
• Identification of R-X-(X)-S/T-X3-S/T as consensus sequence motif for autophosphorylation-dependent protein kinase.
• J Biol Chem. 1995; 270: 3462-3462

• Thummler F, Algarra P, Fobo GM
• Sequence similarities of phytochrome to protein kinases: implication for the structure, function and evolution of the phytochrome gene family.
• FEBS Lett. 1995; 357: 149-55
• Display abstract

• Phytochrome, the best characterised plant photoreceptor, is encoded by a small multigene family within the plant kingdom. The different phytochrome types are composed of a conserved light-sensing chromophore domain of about 80 kDa and a less-conserved C-terminal domain of about 50 kDa. The C-terminus of phytochrome of the moss Ceratodon purpureus is homologous to the catalytic domain of eukaryotic serine/threonine or tyrosine protein kinases; in contrast, for all other phytochromes (conventional phytochromes) sequence similarities within the C-terminal domain to the catalytic domain of bacterial histidine kinases have been reported. We performed careful sequence comparisons of the putative catalytic domains of phytochrome with each other, with authentic serine/threonine, tyrosine and with histidine kinases. We report that conventional phytochromes exhibit structural elements of the catalytic domains of both histidine and, to a lesser extent, of serine/threonine and tyrosine kinases. The significance of these observations is discussed in the framework of the structure, function and evolution of phytochrome.

• Gao G et al.
• Catalytic subunits of the porcine and rat 5'-AMP-activated protein kinase are members of the SNF1 protein kinase family.
• Biochim Biophys Acta. 1995; 1266: 73-82
• Display abstract

• The 5'-AMP-activated protein kinase (AMPK) regulates the fatty acid and sterol synthesizing pathways via phosphorylation of acetyl-CoA carboxylase and HMG-CoA reductase, respectively. Highly purified kinase from porcine liver contains three apparent subunits of molecular mass 63 kDa, 40 kDa and 38 kDa. Peptide sequencing of the 63 kDa protein (AMPK63cat) revealed that this polypeptide is the catalytic subunit of the kinase. Porcine peptide sequences were used to clone by RT-PCR partial length cDNAs for the catalytic domains of the porcine AMPK63cat, and its rat homolog, which were virtually identical in deduced amino acid sequence. Screening of a rat liver cDNA library with these partial length cDNAs and with degenerate oligonucleotides yielded several unique clones, some of which had a 142 bp deletion in the catalytic domain of the kinase. A consensus full-length sequence with a 1.7 kb open reading frame has been constructed from overlapping library and PCR-derived clones. A large mRNA for rat AMPK63cat (8.5 kb) is expressed in nearly all rat tissues, with highest levels detectable in heart and skeletal muscle. Using PCR, the presence of two mRNA species with or without the 142 bp deletion in the catalytic domain was noted in all rat tissues examined. Comparison of the deduced protein sequence of AMPK63cat reveals highly conserved homologies in both the catalytic and non-catalytic domains to several members of the SNF1 kinase family, including kinases from Arabidopsis, barley, rye, and S. cerevesiae, as well as to other mammalian kinases and to a C. elegans kinase. The high evolutionary conservation of both kinase structure and function (metabolite sensing) coupled with their pattern of tissue/organism expression suggest that the mammalian members of this kinase family likely play wider roles than the regulation of cellular lipid metabolism.

• Cooper J, Conner J, Clements JB
• Characterization of the novel protein kinase activity present in the R1 subunit of herpes simplex virus ribonucleotide reductase.
• J Virol. 1995; 69: 4979-85
• Display abstract

• We have compared the protein kinase activities of the R1 subunits from herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) ribonucleotide reductase following expression in Escherichia coli. Autophosphorylation activity was observed when kinase assays were performed with immunoprecipitated R1 or proteins purified to homogeneity, and the activity was stimulated by the basic protein protamine. Transphosphorylation of histones or calmodulin by purified or immunoprecipitated HSV-1 and HSV-2 R1 was not observed, and our results suggest that the activities of these two proteins are similar. We further characterized the protein kinase activity of HSV-1 R1 by producing insertion and deletion mutants constructed with a plasmid expressing R1 amino acids 1 to 449. C-terminal deletion analysis identified the catalytic core of the enzyme as comprising residues 1 to 292, and this polypeptide will be useful for structural determinations by X-ray crystallography. Insertion of a 4-amino-acid sequence at sites within the protein kinase domain identified regions essential for activity; insertions at residues 22 and 112 completely inactivated activity, and an insertion at residue 136 reduced activity sixfold. Similar insertions at residues 257, 262, 292, and 343 had no effect on activity. The ATP analog 5'-fluorosulfonylbenzoyladenosine, which covalently modifies conventional eukaryotic kinases at an essential lysine residue within the active site, did label HSV R1, but this labelling occurred outside the N-terminal domain. These data indicate that the HSV R1 kinase is novel and distinct from other eukaryotic protein kinases.

• Hunter T
• When is a lipid kinase not a lipid kinase? When it is a protein kinase.
• Cell. 1995; 83: 1-4

• Wetterauer BW, Hamker U, von Haeseler A, MacWilliams HK, Simon MN, Veron M
• A protein kinase from Dictyostelium discoideum with an unusual acidic repeat domain.
• Biochim Biophys Acta. 1995; 1265: 97-101
• Display abstract

• DdKinX codes for 1093 amino acids which are organized in four regions: the N-terminal catalytic domain, a region containing 30% acidic amino acids, tandem repeats of the motif VKVEEPVEE and the C-terminus. Identity with other protein kinases is 25 to 30%. Descendent trees show that DdKinX does not belong to any of the known kinase branches.

• Nitabach MN, Macagno ER
• Cell- and tissue-specific expression of putative protein kinase mRNAs in the embryonic leech, Hirudo medicinalis.
• Cell Tissue Res. 1995; 280: 479-89
• Display abstract

• Protein kinases play important roles in various cellular interactions underlying metazoan development. To complement existing analyses of protein kinase function in the development of members of the three phyla, Chordata, Arthropoda, and Nematoda, we have begun to examine the cell- and tissue-specific localization of protein kinases in another metazoan phylum, the Annelida. For this purpose, we used the polymerase chain reaction to amplify putative protein kinase catalytic domain cDNAs from the medicinal leech, Hirudo medicinalis. This strategy allowed us to identify 11 cytoplasmic and receptor tyrosine kinase catalytic domains, and 2 cytoplasmic serine/threonine kinase catalytic domains. Using these cDNAs as probes for nonradioactive whole-mount in situ hybridization, we examined the embryonic expression pattern of each of the corresponding putative kinase mRNAs. As has been found in other species, most of the Hirudo protein kinase mRNAs were expressed in a highly specific manner in certain embryonic cells and tissues. We found both neuron- and glia-specific kinases within the nervous system, as well as kinases expressed in non-nervous tissues, such as the haemocoelomic, muscular, and excretory systems. These kinase cDNAs encode proteins likely to be critical for proper development, and can be used as cell- and tissue-specific histological probes for the analysis of Hirudo embryogenesis.

• Nunoue K, Ohashi K, Okano I, Mizuno K
• LIMK-1 and LIMK-2, two members of a LIM motif-containing protein kinase family.
• Oncogene. 1995; 11: 701-10
• Display abstract

• We previously isolated human cDNA encoding LIM-kinase (LIMK), a putative protein kinase which contains two repeats of the LIM motif at the N-terminus and a protein kinase consensus sequence at the C-terminus. Using as a probe a cDNA fragment of human LIMK, we isolated from a rat brain cDNA library cDNA clones encoding two distinct protein kinases (termed LIMK-1 and LIMK-2) related to human LIMK. LIMK-1 shares with human LIMK 95% of the total 647 amino acids and is probably a rat equivalent of human LIMK. LIMK-2 has an overall sequence and a domain structure similar to that of human LIMK and rat LIMK-1, but overall identity is 50-51% at the amino acid level. Like human LIMK, the protein kinase domains of rat LIMK-1 and -2 contain a characteristic sequence DLNSHN in subdomain VIB and a highly basic insert between subdomain VII and VIII. LIMK-1 and -2 are therefore closely related but distinct members of a novel LIM-containing protein kinase subfamily. Several forms of LIMK-2 transcripts encoding proteins that are N-terminally modified and/or C-terminally truncated are generated by alternative splicing or alternative initiation. Northern blot analysis revealed the expression of LIMK-1 mRNA predominantly in the brain and the expression of LIMK-2 mRNA in various tissues in the rat. Antibody raised against LIMK-1 specifically immunoprecipitated and identified in Rat2 fibroblast cells a 72 kDa protein, which has no detectable autophosphorylating activity but is capable of phosphorylating serine and threonine residues of myelin basic protein, by in vitro kinase reaction. As the LIMK family kinases have unique structural features, they are likely to have specific functions in previously uncharacterized signaling pathways.

• Trigon S, Morange M
• Different carboxyl-terminal domain kinase activities are induced by heat-shock and arsenite. Characterization of their substrate specificity, separation by Mono Q chromatography, and comparison with the mitogen-activated protein kinases.
• J Biol Chem. 1995; 270: 13091-8
• Display abstract

• In response to heat-shock and chemical treatments, cells undergo profound biochemical changes such as modifications in protein phosphorylation in order to resist the new, unfavorable growth conditions. We have previously shown that in HeLa cells a protein kinase (HS-CTD kinase) activity is induced rapidly after a heat or sodium arsenite shock. This kinase activity is able to phosphorylate a synthetic peptide composed of four repeats of the motif Ser-Pro-Thr-Ser-Pro-Ser-Tyr, a motif highly repeated in the carboxyl-terminal domain (CTD) of the largest subunit of eukaryotic RNA polymerase II. In this paper, we designed a new experimental procedure to characterize the substrate specificity of this kinase activity. We show that HS-CTD kinase activity phosphorylates a consensus sequence (-P-X-S/T-P-) which is similar to the sequence phosphorylated by extracellular regulated protein kinases (also called mitogen-activated protein kinases). However, there is a slight but reproducible difference between these kinases in their use of serine or threonine as the phosphate acceptor. Mono Q chromatography allows the separation of five stress-induced CTD kinase activities, two of which coelute with active mitogen-activated protein kinase forms revealed by Western blotting with anti ERK1-ERK2 antibodies. The other three CTD kinase activities induced after a stress are distinct from ERK1 and ERK2 and have different enzymatic properties. The molecular nature of these HS-CTD kinases and the physiological significance of their activation during stress remain to be determined.

• Lee TR, Till JH, Lawrence DS, Miller WT
• Precision substrate targeting of protein kinases v-Abl and c-Src.
• J Biol Chem. 1995; 270: 27022-6
• Display abstract

• The active site substrate specificities of v-Abl and c-Src are compared and contrasted. Both enzymes catalyze the phosphorylation of a broad assortment of peptide-bound aliphatic and aromatic alcohols, such as achiral and simple straight chain residues. In addition, both protein kinases exhibit a "dual specificity" with respect to the ability to utilize D- and L-configurational isomers as substrates. However, c-Src and v-Abl are extremely inefficient as catalysts for certain structural arrangements, including secondary alcohols and primary alcohols containing large substituents in close proximity to the hydroxyl moiety. In addition to these similarities, these enzymes also display noteworthy differences in catalytic behavior. Whereas c-Src exhibits a modest preference for aromatic versus aliphatic alcohols, v-Abl does not. Most dramatic is the ability of c-Src to utilize short chain alcohols as substrates, an activity virtually absent from the catalytic repertoire of v-Abl. The implications of these observations are 2-fold. First, because both enzymes are able to accommodate a wide variety of structural variants within their respective active site regions, there exists a substantial degree of flexibility with respect to inhibitor design. Second, because these enzymes exhibit disparate active site specificities, it is possible that other tyrosine-specific protein kinases will display unique substrate specificities as well. Consequently, it may ultimately be possible to exploit these differences to generate inhibitors that precisely target specific protein kinases.

• Guerrucci MA, Belle R
• Characterisation of protein structure/function relationship by sequence analysis without previous alignment: distinction between sub-groups of protein kinases.
• Biosci Rep. 1995; 15: 161-71
• Display abstract

• Using an approach for protein comparison by computer analysis based on signal treatment methods without previous alignment of the sequence, we have analysed the structure/function relationship of related proteins. The aim was to demonstrate that from a few members of related proteins, specific parameters can be obtained and used for the characterisation of newly sequenced proteins obtained by molecular biology techniques. The analysis was performed on protein kinases, which comprise the largest known family of proteins, and therefore allows valid estimations to be made. We show that using only a dozen defined proteins, the specific parameters extracted from their sequences classified the protein kinase family into two sub-groups: the protein serine/threonine kinases (PSKs) and the protein tyrosine kinases (PTKs). The analysis, largely involving computation, appears applicable to large scale data-bank analysis and prediction of protein functions.

• Arvai AS, Bourne Y, Hickey MJ, Tainer JA
• Crystal structure of the human cell cycle protein CksHs1: single domain fold with similarity to kinase N-lobe domain.
• J Mol Biol. 1995; 249: 835-42
• Display abstract

• The structure of the human CksHs1 homolog of the yeast cell-cycle regulatory proteins suc1 and CKS1, which bind to the catalytic subunit of the cyclin-dependent kinases (Cdks) and are essential for yeast cell-cycle progression in vivo, has been determined at 2.9 A resolution. The CksHs1 single polypeptide domain fold, which consists of a four-stranded beta-sheet flanked by two alpha-helices, is dramatically different from the subunit conformation and assembly of the homologous CksHs2, but strikingly similar to the Cdk N-lobe domain fold. The CksHs1 structure identifies sequence-conserved residues Glu61 to His65 as a novel beta-hinge region that folds back to form a beta-hairpin with CksHs1 subunit, whereas this hinge is unfolded to form an extended beta-strand exchange between two CksHs2 subunits. Phosphate and the phosphate analog metavanadate bind CksHs1 in a shallow pocket and interact with five conserved residues (Lys11, Arg20, Ser51, Trp54 and Arg71) suggesting a specific Cks recognition site for a phosphorylated Cdk residue. The dramatic changes to the Cks fold, assembly and exposed conserved surface brought about by switching between the bent and extended hinge conformations are potentially important for the functions of this Cks homolog and could explain conflicting activities inferred from different types of genetic experiments.

• Omura S, Sasaki Y, Iwai Y, Takeshima H
• Staurosporine, a potentially important gift from a microorganism.
• J Antibiot (Tokyo). 1995; 48: 535-48

• Bossemeyer D
• The glycine-rich sequence of protein kinases: a multifunctional element.
• Trends Biochem Sci. 1994; 19: 201-5
• Display abstract

• Evolution favours the use of glycine-rich loops for nucleotide binding in proteins. In the large family of protein kinases, the catalytic domain of which has one of the highest degrees of conservation among all known proteins, the structure of the nucleotide-binding site differs from classical folds. We are now beginning to understand the multiple functional roles of the glycine-rich sequence in protein kinases and some of the structural constraints leading to its conservation.

• Hunter T
• 1001 protein kinases redux--towards 2000.
• Semin Cell Biol. 1994; 5: 367-76
• Display abstract

• Recent genomic analysis indicates that the number of protein kinase genes in eukaryotes may be higher than previously thought, and vertebrate genomes may contain in the vicinity of 2000. In addition to the growing protein-serine/protein-tyrosine kinase superfamily, new types of protein kinase have been discovered that operate on different structural principles. The structures of four protein-serine kinases have been solved and have revealed a common structural core containing the highly conserved residues in the catalytic domain. These structures provide insights into substrate selectivity and protein kinase activation. New regulatory principles for protein kinase have been uncovered, including phosphorylation of residues within the catalytic domain by a second protein kinase, new second messengers and specific protein inhibitors. Evidence that protein kinase cascades play an important role in signal transduction has emerged. A number of fundamental cellular processes such as the cell cycle and transcription have been shown to require protein phosphorylation.

• Vihinen M et al.
• Structural basis for chromosome X-linked agammaglobulinemia: a tyrosine kinase disease.
• Proc Natl Acad Sci U S A. 1994; 91: 12803-7
• Display abstract

• X-linked agammaglobulinemia (XLA) is a hereditary defect of B-cell differentiation in man caused by deficiency of Bruton tyrosine kinase (BTK). A three-dimensional model for the BTK kinase domain, based on the core structure of cAMP-dependent protein kinase, was used to interpret the structural basis for disease in eight independent point mutations in patients with XLA. As Arg-525 of BTK has been thought to functionally substitute for a critical lysine residue in protein-serine kinases, the mutation Arg-525-->Gln was studied and found to abrogate the tyrosine kinase activity of BTK. All of the eight mutations (Lys-430-->Glu, Arg-520-->Glu, Arg-525-->Gln, Arg-562-->Pro, Ala-582-->Val, Glu-589-->Gly, Gly-594-->Glu, and Gly-613-->Asp) were located on one face of the BTK kinase domain, indicating structural clustering of functionally important residues.

• Veron M, Radzio-Andzelm E, Tsigelny I, Taylor S
• Protein kinases share a common structural motif outside the conserved catalytic domain.
• Cell Mol Biol (Noisy-le-grand). 1994; 40: 587-96
• Display abstract

• A comparison of the sequences of the mammalian and Dictyostelium catalytic subunits of cAMP-dependent protein kinase revealed extensive sequence similarities through the catalytic core and the carboxy terminal tail. The amino terminal sequences however differ dramatically. The large difference in size, 73 kDa for the Dictyostelium enzyme versus 40 kDa is due to an extension in the N-terminus. The mouse enzyme has at its amino-terminus a long amphipatic helix, the A-helix, that precedes the catalytic core, covering the surface of both lobes of the enzyme. Dictyostelium does in fact, have a similar motif but it is remote from the catalytic core, in the N-terminal extension. On the basis of molecular modeling, it is proposed that residues 77-98 correspond to a structural motif similar to the A-helix in mouse catalytic subunit. Sequences encoding similar putative motifs contiguous to the catalytic core can be recognized in many other protein kinases and is particularly prominent in all of the non-receptor tyrosine kinases. In the case of Src, this A-helix motif appears to serve as the linker between the conserved catalytic core and the SH2 domain. The interaction between the A-helix motif and the core is described, and the general occurrence of this structure within the protein kinase family is discussed.

• Cox S, Radzio-Andzelm E, Taylor SS
• Domain movements in protein kinases.
• Curr Opin Struct Biol. 1994; 4: 893-901
• Display abstract

• Structural studies of the catalytic subunit of the cAMP-dependent protein kinase, both by crystallographic methods and in solution, reveal two conformations. Crystal structures of several other protein kinases have also been solved in the past year. With this combined information we can begin to define mobile domains and subdomains within the conserved catalytic core.

• Goldsmith EJ, Cobb MH
• Protein kinases.
• Curr Opin Struct Biol. 1994; 4: 833-40
• Display abstract

• The structures of four serine/threonine protein kinases have been determined recently. By comparing these structures with that of the cAMP-dependent protein kinase (cAPK), it is now possible to see how the activity of these regulatory enzymes is controlled. Low activity is maintained through the conformation of the phosphorylation lip, domain rotations, and binding of substrate analog inhibitors and autoinhibitory domains.

• Kemp BE, Parker MW, Hu S, Tiganis T, House C
• Substrate and pseudosubstrate interactions with protein kinases: determinants of specificity.
• Trends Biochem Sci. 1994; 19: 440-4
• Display abstract

• Protein crystallography has revealed that protein kinases have extended protein-substrate-binding grooves associated with their active sites. Some protein kinases are autoinhibited by a mechanism in which part of their structure, termed a pseudosubstrate, occupies the active site. Substrates and pseudosubstrates occupy overlapping regions within the extended substrate-binding groove, making multiple specific electrostatic and non-polar contacts. With masterly economy, Nature has exploited the active site in many protein kinases to both recognize substrates with great specificity and autoregulate by remaining inactive until the appropriate activation signal is received.

• Taylor SS, Knighton DR, Zheng J, Sowadski JM, Gibbs CS, Zoller MJ
• A template for the protein kinase family.
• Trends Biochem Sci. 1993; 18: 84-9
• Display abstract

• The crystal structure of the catalytic subunit of cAMP-dependent protein kinase, complexed with ATP and a 20-residue inhibitor peptide, is reviewed and correlated with chemical and genetic data. The striking convergence of the structure with the biochemistry and genetics provides for the first time a molecular basis for understanding how this enzyme functions, as well as an explanation for the highly conserved residues that are scattered throughout the molecule. Because these residues probably serve a common role in all eukaryotic protein kinases, this first protein kinase structure serves as a general template for the entire family of enzymes.

• Mushegian AR, Koonin EV
• The proposed plant connexin is a protein kinase-like protein.
• Plant Cell. 1993; 5: 998-9

• Taylor SS et al.
• cAMP-dependent protein kinase defines a family of enzymes.
• Philos Trans R Soc Lond B Biol Sci. 1993; 340: 315-24
• Display abstract

• The structure of the recombinant mouse catalytic subunit of cAMP-dependent protein kinase is reviewed with particular emphasis on the overall features and specific amino acids that are shared by all members of the eukaryotic protein kinase family. The crystal structure of a ternary complex containing both MgATP and a twenty-residue inhibitor peptide defines the precise role of the conserved residues that are clustered at the active site. In addition to catalysing the post-translational modification of other proteins, the catalytic subunit is itself subject to covalent modifications. It is a phosphoprotein and is also myristylated at its amino terminus. The enzyme when crystallized in the presence of detergent shows a detergent molecule bound to an acyl pocket that is presumably occupied by the myristyl moiety in the mammalian enzyme. When expressed in E. coli, the catalytic subunit is autophosphorylated at four sites. Two stable phosphates at Ser338 and Thr197 interact with multiple protein side chains thus explaining why they are inaccessible to phosphatases. Although all substrates and inhibitors of the catalytic subunit share a general minimum consensus sequence, the high affinity binding of protein inhibitors such as the regulatory subunits and the heat stable protein kinase inhibitors require additional determinants that lie beyond the consensus site. These two physiological inhibitors of the catalytic subunit appear to use different sites to achieve high-affinity binding.

• Veron M, Radzio-Andzelm E, Tsigelny I, Ten Eyck LF, Taylor SS
• A conserved helix motif complements the protein kinase core.
• Proc Natl Acad Sci U S A. 1993; 90: 10618-22
• Display abstract

• Residues 40-300 of the mammalian catalytic (C) subunit of cAMP-dependent protein kinase define a conserved bilobal catalytic core shared by all eukaryotic protein kinases. Contiguous to the core is an extended amphipathic alpha-helix (A helix). Trp30, a prominent feature of this helix, fills a deep hydrophobic pocket between the two lobes on the surface opposite to the active site. The C subunit in Dictyostelium discoideum shows sequence conservation of residues 40-350 with the mouse enzyme but contains an N-terminal extension of 332 residues. A sequence corresponding to the A helix contiguous to the core is absent. However, we have now identified a remote A-helix motif (residues 77-98). When the core of the Dictyostelium C subunit was modeled, based on the mouse C subunit, complementarity between this putative A helix and the surface of the core was found to be conserved. Analysis of other protein kinases reveals that the A-helix motif is not restricted to cAMP-dependent protein kinase. In the Src-related family of protein kinases, for example, an A helix is very likely contiguous to the core, thus serving as a linker between the conserved catalytic core and the Src homology 2 domain. We predict that an A-helix motif complementary to the core will be a conserved feature of most eukaryotic protein kinases.

• Wu J, Michel H, Dent P, Haystead T, Hunt DF, Sturgill TW
• Activation of MAP kinase by a dual specificity Tyr/Thr kinase.
• Adv Second Messenger Phosphoprotein Res. 1993; 28: 219-25

• Roberts DM
• Protein kinases with calmodulin-like domains: novel targets of calcium signals in plants.
• Curr Opin Cell Biol. 1993; 5: 242-6
• Display abstract

• Recently, a novel calcium-dependent protein kinase has been identified that is structurally distinguished by the localization of a calcium-binding regulatory domain fused to a serine/threonine catalytic domain. The regulatory domain is homologous to calmodulin and contains four helix-loop-helix calcium-binding sites. As a result, the kinase is directly activated by calcium without a requirement for other effector molecules.

• Taylor SS et al.
• Crystal structures of the catalytic subunit of cAMP-dependent protein kinase reveal general features of the protein kinase family.
• Receptor. 1993; 3: 165-72
• Display abstract

• The crystal structure of the catalytic subunit of cAMP-dependent protein kinase serves as a template for the catalytic core of all eukaryotic protein kinases. The various crystal structures are reviewed with particular emphasis on the numerous conserved residues that converge at the active site. The structures also reveal the importance of posttranslational modifications, including myristylation and phosphorylation.

• Bork P, Sander C
• A hybrid protein kinase-RNase in an interferon-induced pathway?
• FEBS Lett. 1993; 334: 149-52
• Display abstract

• The sequence of RNase L has been re-examined by computer analysis. We propose a molecular architecture of RNase L, with an unusual combination, in one protein chain, of 9 ankyrin-like repeats, a functional active protein kinase and a C-terminal catalytic RNase similar to the yeast protein, IRE1. The protein kinase may be involved in a new signal transduction pathway which remains to be discovered.

• Butt E, Geiger J, Jarchau T, Lohmann SM, Walter U
• The cGMP-dependent protein kinase--gene, protein, and function.
• Neurochem Res. 1993; 18: 27-42

• Sullivan V, Talarico CL, Stanat SC, Davis M, Coen DM, Biron KK
• A protein kinase homologue controls phosphorylation of ganciclovir in human cytomegalovirus-infected cells.
• Nature. 1992; 359: 85-85

• Hofmann F, Dostmann W, Keilbach A, Landgraf W, Ruth P
• Structure and physiological role of cGMP-dependent protein kinase.
• Biochim Biophys Acta. 1992; 1135: 51-60

• Taylor SS, Knighton DR, Zheng J, Ten Eyck LF, Sowadski JM
• Structural framework for the protein kinase family.
• Annu Rev Cell Biol. 1992; 8: 429-62
• Display abstract

• In this review, we have summarized the general structural features of the catalytic subunit of cAMP-dependent protein kinase, emphasizing those features that will very likely be conserved in all members of the protein kinase family. The overall secondary structure of the catalytic core will probably be conserved throughout the catalytic core, as will the active site regions associated with MgATP binding and catalysis. The mechanisms for activation and the role of protein phosphorylation are unique for each kinase. The structure of the catalytic subunit now provides a general framework for modeling other protein kinases. Although this is no substitute for a crystal structure for each protein kinase, this one structure, nevertheless, does provide major insights to the molecular organization of each of these enzymes.

• Walsh DA, Glass DB, Mitchell RD
• Substrate diversity of the cAMP-dependent protein kinase: regulation based upon multiple binding interactions.
• Curr Opin Cell Biol. 1992; 4: 241-51
• Display abstract

• The proposition is forwarded that the cAMP-dependent protein kinase is one of quite a small class of enzymes wherein differential modes of binding of its multiple substrates make an important contribution to the end physiological response. It is postulated that a variety of different substrate affinities may have evolved in order to regulate the order of substrate phosphorylation. The recent elucidation of the protein's three-dimensional structure provides the opening to test this as a new concept of cellular regulation.

• Huggins JP, Landgraf W, Hofmann F, Pelton JT
• Secondary structure and conformational changes associated with substrate-binding and the N-terminus in cyclic GMP-dependent protein kinase.
• Biochem Soc Trans. 1991; 19: 163-163

• Hoffman M
• First protein kinase structure.
• Science. 1991; 253: 383-383

• Benner SA, Gerloff D
• Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases.
• Adv Enzyme Regul. 1991; 31: 121-81
• Display abstract

• The secondary structure and elements of tertiary structure have been predicted for the catalytic domain of protein kinases using a method that extracts structural information from the patterns of conservation and variation in an alignment of homologous proteins. The central features of this structural prediction are: (a) the catalytic domains of protein kinases do not incorporate a Rossmann fold; (b) the core of the structure is founded on beta sheets built from pairs of bent antiparallel beta strands; (c) five helices, including an especially long helix (alignment positions 129-152) that lie on the outside of the folded core. These proteins are important in many aspects of metabolic regulation.

• Huggins JP, Pelton JT
• Predictions of cyclic GMP-dependent protein kinase structure from its primary sequence.
• Biochem Soc Trans. 1991; 19: 162-162

• Tuazon PT, Traugh JA
• Casein kinase I and II--multipotential serine protein kinases: structure, function, and regulation.
• Adv Second Messenger Phosphoprotein Res. 1991; 23: 123-64

• Gibbs CS, Zoller MJ
• Rational scanning mutagenesis of a protein kinase identifies functional regions involved in catalysis and substrate interactions.
• J Biol Chem. 1991; 266: 8923-31
• Display abstract

• A systematic mutagenesis strategy was used to identify the functional regions and residues of a protein kinase. Clusters of the charged amino acids in the catalytic subunit of Saccharomyces cerevisiae cAMP-dependent protein kinase, were systematically mutated to alanine, producing a set of mutations that encompassed the entire molecule. Residues indispensable for enzyme activity were identified by testing the ability of the mutants to function in vivo. Active mutants were assayed in vitro, and mutants with reduced specific activity were subsequently analyzed by steady-state kinetics to determine the effects of the mutation on kcat and on Km for MgATP and for a peptide substrate. Specific residues and regions of the enzyme were identified that are likely to be important in catalysis and in binding of MgATP, functions that are common to all protein kinases. Additional regions were identified that are likely to be important in binding a peptide substrate, the recognition of which is likely to be specific to the serine/threonine protein kinases that have a requirement for basic residues around the target hydroxyamino acid. The properties of mutants defective in substrate recognition were consistent with an ordered sequential reaction mechanism. This represents the first comprehensive analysis of a protein kinase by a rational mutagenesis strategy.

• Jones PF, Jakubowicz T, Hemmings BA
• Molecular cloning of a second form of rac protein kinase.
• Cell Regul. 1991; 2: 1001-9
• Display abstract

• A novel serine/threonine protein kinase (termed rac-PK) has recently been identified and cloned from cDNA libraries derived from the human cell lines MCF-7 and WI38. A second form of this protein kinase, termed rac protein kinase beta, has been identified from cDNAs derived from the same cell lines. These two closely related forms show 90% homology, although the beta form with a predicted Mr 60,200 has a carboxyl terminal extension of 40 amino acids in comparison to the alpha form. This extension has a high serine content with 11 serine residues in the last 30 amino acids. The beta form of the protein has been shown by both in vitro translation and bacterial expression to be approximately 5000 Da larger than the alpha form. rac protein kinase beta is encoded by a 3.4-kb transcript and the alpha form is encoded by a 3.2-kb mRNA. Using gene-specific probes both transcripts were detected in all cell types analyzed, although levels of expression were different for the two forms. The catalytic domain of rac protein kinase beta shows a high degree of homology to both the protein kinase C and cyclic AMP-dependent protein kinase families, and hence rac protein kinases appear to represent a new subfamily of the second messenger serine/threonine protein kinases.

• Kidd VJ et al.
• Regulated expression of a cell division control-related protein kinase during development.
• Cell Growth Differ. 1991; 2: 85-93
• Display abstract

• Protein kinases are important signaling molecules that are known constituents of cellular pathways critical for normal cellular growth and development. We have recently identified a new protein kinase, p58, which contains a large domain that is highly homologous to the cell division control p34cdc2 protein kinase. This new cell division control-related protein kinase was originally identified as a component of semipurified galactosyltransferase; thus, it has been denoted galactosyltransferase-associated protein kinase. In vitro, this protein kinase has been shown to phosphorylate a number of substrates, including histone H1, casein, and galactosyltransferase. In vivo, we have found that this protein kinase affects galactosyltransferase enzyme activity and that it is apparently involved in some aspect of normal cell cycle regulation. In this report, we find that the p58 gene is evolutionarily well conserved and expressed ubiquitously, but to varying extents, in adult tissues. In developmentally staged embryos, p58 expression was elevated early in embryogenesis and then decreased dramatically. In the murine submandibular gland, p58 expression was elevated between day 14 and day 16 post coitus. Expression in the submandibular gland appeared to parallel the proliferation and differentiation of specific cell types as judged by in situ hybridization. These studies indicate that the p58 protein kinase may have a critical function during normal embryonic development and that this protein kinase continues to be expressed in differentiated adult tissues.

• Hagedorn CH
• Use of a monoclonal antibody (APE-1) directed against the conserved GTPEYLAPE motif present in protein kinases as an affinity purification reagent.
• FEBS Lett. 1991; 291: 29-32
• Display abstract

• cDNA sequence studies have predicted the existence of protein kinases that have not been characterized at the protein level. This laboratory has previously shown that polyclonal rabbit antibodies directed against a highly conserved sequence motif, GTPEYLAPE, present in the catalytic domain of many protein kinases will react during immunoblots with several protein kinases containing the same or homologous motifs. In this report I describe the development of a mouse monoclonal antibody, designated APE-1, that reacts with the GTPEYLAPE motif. In addition, the use of this monoclonal antibody in the affinity purification of kinase activities from rabbit reticulocyte lysate is described. This approach may provide a general method for the purification of previously uncharacterized protein kinases that share regions which are homologous to the GTPEYLAPE motif. Refinements in this method may permit the rapid purification of nonabundant and/or rapidly inactivated protein kinases that have not been isolated using other approaches.

• Buechler JA, Toner-Webb JA, Taylor SS
• Carbodiimides as probes for protein kinase structure and function.
• Methods Enzymol. 1991; 200: 487-500

• Pearson RB, Kemp BE
• Protein kinase phosphorylation site sequences and consensus specificity motifs: tabulations.
• Methods Enzymol. 1991; 200: 62-81

• Hanks SK, Quinn AM
• Protein kinase catalytic domain sequence database: identification of conserved features of primary structure and classification of family members.
• Methods Enzymol. 1991; 200: 38-62

• Adams V, Griffin LD, Gelb BD, McCabe ER
• Protein kinase activity of rat brain hexokinase.
• Biochem Biophys Res Commun. 1991; 177: 1101-6
• Display abstract

• Hexokinase 1 (HK1) purified from rat brain exhibits protein kinase activity, including autophosphorylation and phosphorylation of histone H2A. This protein kinase activity is observed only in the absence of the HK1 carbohydrate substrate, glucose. Analysis of the ATP-binding domains of the mammalian HK1 protein sequences shows significant homology with other mammalian protein kinases.

• Lees-Miller SP, Anderson CW
• The DNA-activated protein kinase, DNA-PK: a potential coordinator of nuclear events.
• Cancer Cells. 1991; 3: 341-6
• Display abstract

• DNA-PK is a moderately abundant serine/threonine protein kinase found in the nucleus of a wide range of eukaryotic cells. It is one of the few known cellular enzymes whose activity is regulated directly by DNA. Many DNA binding proteins, including a number of transcription factors, are substrates for DNA-PK in vitro. We suggest that this kinase may coordinate signal transduction pathways and nuclear events, including transcription, in response to changes in DNA or chromatin state.

• Soderling TR
• Protein kinases. Regulation by autoinhibitory domains.
• J Biol Chem. 1990; 265: 1823-6

• Hagedorn CH, Tettelbach WH, Panella HL
• Development and characterization of polyclonal antibodies against a conserved sequence in the catalytic domain of protein kinases.
• FEBS Lett. 1990; 264: 59-62
• Display abstract

• Using a synthetic oligopeptide (CGGGTPEYLAPEGGK) crosslinked to keyhole limpet hemocyanin we have raised polyclonal rabbit antibodies against a 9 residue homologous region found in the catalytic domain of most protein kinases. These antibodies reacted during Western immunoblotting with cAMP dependent protein kinase catalytic subunit, phosphorylase kinase gamma subunit and calcium calmodulin dependent protein kinase II which have homologous sequences of GTPEYLAPE, GTPSYLAPE and GTPGYLSPE, respectively. Five other protein kinases did not react with anti-GTPEYLAPE antibodies during Western immunoblotting. Affinity-purified antibodies were able to detect as little as 50 ng of cAMP dependent protein kinase and 200 ng of Ca2+/calmodulin dependent protein kinase II. Immunoblotting of A431 cell plasma membrane vesicles indicated the presence of an approximately 55 kDa protein that contains the conserved sequence and is likely to be a protein kinase. Antibodies directed against conserved sequences present in protein kinases, or possibly other enzymes, may be useful in identifying previously uncharacterized enzymes at the protein level.

• Taylor SS, Buechler JA, Yonemoto W
• cAMP-dependent protein kinase: framework for a diverse family of regulatory enzymes.
• Annu Rev Biochem. 1990; 59: 971-1005
• Display abstract

• cAPK has provided many insights into the functioning of the diverse family of eukaryotic protein kinases. The fact that a particular amino acid in the catalytic core is conserved is an indication that the residue plays an important role; however, questions concerning function remain obscure. With the catalytic subunit, the assignment of amino acids that participate in catalysis has begun, and in many instances that function appears to be conserved in the other protein kinases. Although the regulatory subunit and the use of cAMP to release its inhibitor effects is unique to cAPK, the general mechanism of a small autoinhibitory region occupying the peptide binding site and thus preventing access of other substrates may be invoked frequently by other protein kinases. Coupling recombinant approaches with protein chemistry is allowing us to decipher at least some of the molecular events associated with cAMP-binding and holoenzyme activation. Although the next chapter in the history of cAPK will undoubtedly include three-dimensional structures, the chemical information remains as an essential complement for interpreting those structures and eventually understanding the molecular events associated with catalysis and activation.

• Banerjee P, Ahmad MF, Grove JR, Kozlosky C, Price DJ, Avruch J
• Molecular structure of a major insulin/mitogen-activated 70-kDa S6 protein kinase.
• Proc Natl Acad Sci U S A. 1990; 87: 8550-4
• Display abstract

• The molecular structure of a rat hepatoma 70-kDa insulin/mitogen-stimulated S6 protein kinase, obtained by molecular cloning, is compared to that of a rat homolog of the 85-kDa Xenopus S6 protein kinase alpha; both kinases were cloned from H4 hepatoma cDNA libraries. The 70-kDa S6 kinase (calculated molecular mass of 59,186 Da) exhibits a single catalytic domain that is most closely related in amino acid sequence (56% identity) to the amino-terminal, kinase C-like domain of the rat p85 S6 kinase (calculated molecular mass of 82,695 Da); strong similarity extends through a further 67 residues carboxyl-terminal to the catalytic domain (40% identity), corresponding to a region also conserved among the kinase C family. Outside of this segment of approximately 330 amino acids, the structures of the p70 and p85 S6 kinases diverge substantially. The p70 S6 kinase is known to be activated through serine/threonine phosphorylation by unidentified insulin/mitogen-activated protein kinases. A model for the regulation of p70 S6 protein kinase activity is proposed wherein the low activity of the unphosphorylated enzyme results from the binding of a basic, inhibitory pseudosubstrate site (located carboxyl-terminal to the extended catalytic domain) to an acidic substrate binding region (located amino-terminal to the catalytic domain); substrate binding is thereby prevented. S6 kinase activation requires displacement of this inhibitory segment, which is proposed to occur consequent to its multiple phosphorylation. The putative autoinhibitory segment contains several serine and threonine residues, each followed directly by a proline residue. This motif may prevent autophosphorylation but permit transphosphorylation; two of these serine residues reside in a maturation promoting factor (MPF)/cdc-2 consensus motif. Thus, hormonal regulation of S6 kinase may involve the action of MPF/cdc-2 or protein kinases with related substrate specificity.

• Dobrowolska G
• [The structure and properties of casein kinases]
• Postepy Biochem. 1989; 35: 231-44

• Dadssi M, Duclos B, Cozzone AJ
• A peptide substrate for Escherichia coli protein kinase activity in vitro.
• Biochem Biophys Res Commun. 1989; 160: 552-8
• Display abstract

• The phosphorylation in vitro of a series of exogenous peptides by E. coli protein kinases was studied. One of the substrates assayed, the hexapeptide Arg-Gly-Tyr-Ser-Leu-Gly, was found to be significantly phosphorylated at its serine residue. This finding provides the first example of an exogenous substrate utilizable by bacterial protein kinases. The kinetic parameters of the corresponding reaction were determined and the effect of various cations were analyzed. Magnesium, cobalt, manganese and zinc ions were all found to be activators, although to a varying extent. The results were discussed in terms of substrate specificity of bacterial protein kinases.

• Gasior E
• [Protein kinases and their structural and functional similarities and differences]
• Postepy Biochem. 1989; 35: 211-7

• Folkers G, Krickl S, Trumpp S
• [Localization of the essential structure for binding of antiviral agents to thymidine kinase by studying sequence homologies]
• Arch Pharm (Weinheim). 1989; 322: 409-13
• Display abstract

• The amino acid sequence of 14 thymidine kinases and three other nucleotide binding enzymes have been compared by alignment of their primary and secondary structure. The overall alignment revealed five homologous regions, which are supposed to be part of the active site with a common three dimensional structure. Analysis of mutant enzymes brings further evidence for the importance of those regions. Single point mutations are responsible for an amino acid exchange within the homologous sequences thereby affecting the normal function of the enzymes. The substituted amino acids are essential for the binding function and, therefore, building part of an active site. After identification of the homologous regions we tried to fit the HSV 1 thymidine kinase on the known 3D-structure of adenylate kinase to reconstruct the essential binding regions of thymidine kinase as far as possible.

• Mannermaa RM, Oikarinen J
• Homology of nuclear factor I with the protein kinase family.
• Biochem Biophys Res Commun. 1989; 162: 427-34
• Display abstract

• It is observed that a putative DNA binding domain in nuclear factor I (NF I) which is a eukaryotic sequence-specific DNA binding protein participating in both regulation of DNA replication and transcription displays sequence homology with catalytic domains in various protein kinases. In addition, hydropathy analysis reveals that the NF I polypeptide chain is likely to fold into similar secondary and tertiary structures to those of the protein kinases. Although it is not known whether NF I functions as a protein kinase in addition to recognizing a specific sequence on DNA, it is concluded that some of the eukaryotic DNA binding proteins and protein kinases may belong to a gene family, various members of which are evolutionarily related and responsible for the regulation of metabolism in diverse compartments of the cell. The present finding also suggests that a number of kinases may to varying extents be capable of direct interaction with DNA.

• Ristiniemi J, Oikarinen J
• Homology of histone H1 variants with adenine nucleotide-binding proteins.
• Biochem Biophys Res Commun. 1988; 153: 783-91
• Display abstract

• Significant homology was observed between the adenine nucleotide-binding domain in the catalytic subunit of bovine protein kinase A and the carboxy-terminal half of the globular domain of histone H1. A consensus sequence deducible from several previously characterized adenine nucleotide-binding sites is totally conserved in H1. In addition, several putative phosphate binding-sites were observed within the carboxyterminal tail and one in the cluster of basic amino acids in the aminoterminal tail. Both the putative adenine and phosphate-binding sites are well conserved through evolution in various species and in different H1 variants. The present data thus suggest that histone H1 variants may bind to adenine derivatives and imply that they may recognize a specific nucleotide sequence in DNA.

• Francis SH, Woodford TA, Wolfe L, Corbin JD
• Types I alpha and I beta isozymes of cGMP-dependent protein kinase: alternative mRNA splicing may produce different inhibitory domains.
• Second Messengers Phosphoproteins. 1988; 12: 301-10
• Display abstract

• We recently described a novel isozyme of cGMP-dependent protein kinase (type I beta). It has a structure and peptide substrate specificity which is similar to that of type I alpha, but it has a different cGMP binding behavior, and autophosphorylation occurs almost entirely in serine instead of in both serine and threonine residues (Wolfe, L., Corbin, J.D., and Francis, S.H. (1989) J. Biol. Chem. 264, 7734-7741). An amino-terminal sequence of 31 amino acids derived from three proteolytic fragments of type I beta had 45% homology with a sequence beginning at type I alpha-47. However, sequences of three CNBr peptides of type I beta were identical to sequences of type I alpha beginning at type I alpha-202, -213, and -576 of 11, 27, and 30 residues. These sequences include portions of the catalytic domain and at least one cGMP-binding domain (site 1). Thus, types I alpha and I beta may be produced by alternative splicing of two unique mRNA segments to generate different amino acid sequences in the protein in a region that is amino-terminal to type I alpha-202. This segment in type I beta corresponds to the region in type I alpha that includes the major autophosphorylation site (Thr-58) which is within the domain that is proposed to inhibit catalytic activity. This region presumably interacts with the cGMP-binding site(s) to account for the differences in cGMP-binding behavior between types I alpha and I beta. Even though the sequence of type I beta in the variable region lacks the residue corresponding to Thr-58, it includes a consensus phosphorylation site (KRQAISA) beginning at type I alpha-59, which is absent in type I alpha. The results imply flexibility in the design of the autophosphorylation site and, hence, of the inhibitory domain.

• Taylor SS et al.
• CAMP-dependent protein kinase: prototype for a family of enzymes.
• FASEB J. 1988; 2: 2677-85
• Display abstract

• Protein kinases represent a diverse family of enzymes that play critical roles in regulation. The simplest and best-understood biochemically is the catalytic (C) subunit of cAMP-dependent protein kinase, which can serve as a framework for the entire family. The amino-terminal portion of the C subunit constitutes a nucleotide binding site based on affinity labeling, labeling of lysines, and a conserved triad of glycines. The region beyond this nucleotide fold also contains essential residues. Modification of Asp 184 with a hydrophobic carbodiimide leads to inactivation, and this residue may function as a general base in catalysis. Despite the diversity of the kinase family, all share a homologous catalytic core, and the residues essential for nucleotide binding or catalysis in the C subunit are invariant in every protein kinase. Affinity labeling and intersubunit cross-linking have localized a portion of the peptide binding site, and this region is variable in the kinase family. The crystal structure of the C subunit also is being solved. The C subunit is maintained in its inactive state by forming a holoenzyme complex with an inhibitory regulatory (R) subunit. This R subunit has a well-defined domain structure that includes two tandem cAMP binding domains at the carboxy-terminus, each of which is homologous to the catabolite gene activator protein in Escherichia coli. Affinity labeling with 8N3 cAMP has identified residues that are in close proximity to the cAMP binding sites and is consistent with models of the cAMP binding sites based on the coordinates of the CAP crystal structure. An expression vector was constructed for the RI subunit and several mutations have been introduced. These mutations address 1) the major site of photoaffinity labeling, 2) a conserved arginine in the cAMP binding site, and 3) the consequences of deleting the entire second cAMP binding domain.

• Hanks SK, Quinn AM, Hunter T
• The protein kinase family: conserved features and deduced phylogeny of the catalytic domains.
• Science. 1988; 241: 42-52
• Display abstract

• In recent years, members of the protein kinase family have been discovered at an accelerated pace. Most were first described, not through the traditional biochemical approach of protein purification and enzyme assay, but as putative protein kinase amino acid sequences deduced from the nucleotide sequences of molecularly cloned genes or complementary DNAs. Phylogenetic mapping of the conserved protein kinase catalytic domains can serve as a useful first step in the functional characterization of these newly identified family members.

• Jones SW, Erikson E, Blenis J, Maller JL, Erikson RL
• A Xenopus ribosomal protein S6 kinase has two apparent kinase domains that are each similar to distinct protein kinases.
• Proc Natl Acad Sci U S A. 1988; 85: 3377-81
• Display abstract

• We report the molecular cloning of cDNAs for S6 kinase II (S6KII) mRNAs present in Xenopus ovarian tissue. Two cDNAs were isolated by hybridization to oligonucleotide probes designed to encode tryptic peptides isolated from S6KII. The two cDNAs show 91% sequence similarity to each other. These two cDNAs predict proteins of 733 (S6KII alpha) and 629 (S6KII beta) amino acids that show 95% sequence similarity over the 629 amino acids where they are colinear. Amino acids 44-733 of S6KII alpha were expressed in Escherichia coli and the recombinant protein was used to raise antiserum in rabbits. This antiserum reacted with authentic S6KII prepared from Xenopus eggs. This interaction was specifically blocked by the recombinant protein from E. coli. The sequences of S6KII alpha and -beta predict four tryptic peptides whose sequences are identical to four peptides isolated from a tryptic digest of S6KII. The S6KII proteins have a very unusual structure when compared with previously studied protein kinases. They contain two apparent kinase domains, each similar to distinct protein kinases. The amino-terminal 366 amino acids show high sequence similarity to the regions of protein kinase C, the catalytic subunit of cAMP-dependent protein kinase, and cGMP-dependent protein kinase that contain the sites for ATP binding and are believed to be the catalytic centers for phosphotransferase activity. The remainder of the S6 kinase molecule shows high sequence similarity to the ATP-binding and presumed catalytic domain of the catalytic subunit of phosphorylase b kinase.

• Bairoch A, Claverie JM
• Sequence patterns in protein kinases.
• Nature. 1988; 331: 22-22

• Samuel KP, Seth A, Konopka A, Lautenberger JA, Papas TS
• The 3'-orf protein of human immunodeficiency virus shows structural homology with the phosphorylation domain of human interleukin-2 receptor and the ATP-binding site of the protein kinase family.
• FEBS Lett. 1987; 218: 81-6
• Display abstract

• The primary amino acid sequence within a stretch of 25 residues (positions 91-116) of the middle portion of the 3'-orf protein (p27(3')-orf) of the human immunodeficiency virus (HIV) shares structural homology with a highly charged region within the intracytoplasmic phosphorylation domain of human interleukin-2 receptor (IL-2R) and the ATP-binding site of the catalytic subunit of cAMP-dependent protein kinase (cAMP-PK) and other members of the protein kinase family. Comparison of the predicted secondary structure within this region of p27(3')-orf with the phosphorylation domain of human IL-2R and the ATP-binding region of the phospho-kinase family of protein suggests that the 3'-orf protein could serve homologous function(s).

• Ohno S, Aoshima M, Matsumoto S, Yahara I, Suzuki K
• A yeast gene coding for a putative protein kinase homologous to cdc25 suppressing protein kinase.
• FEBS Lett. 1987; 222: 279-85
• Display abstract

• A yeast gene termed YKR coding for a putative protein kinase was isolated by using the cloned cDNA for rabbit protein kinase C as a hybridization probe. The encoded protein (YKR), composed of 380 amino acid residues, shows extensive sequence homology to serine/threonine-specific protein kinases from various species in the approx. 320 C-terminal amino acid residues, strongly suggesting that YKR is endowed with a protein kinase activity. The observed homologies to the cdc25 suppressing protein kinase from yeast, the catalytic subunit of mammalian cAMP-dependent protein kinase, and mammalian protein kinase C were 76, 48 and 37%, respectively. Gene replacement experiments showed that YKR itself is not essential for cell proliferation.

• Kaiser ET
• Studies on the mechanism of action of phosphoryl transferase enzymes.
• Biochem Soc Trans. 1987; 15: 1187-8

• Naharro G, Robbins KC, Reddy EP
• Gene product of v-fgr onc: hybrid protein containing a portion of actin and a tyrosine-specific protein kinase.
• Science. 1984; 223: 63-6
• Display abstract

• The nucleotide sequence of the region of Gardner-Rasheed feline sarcoma virus (GR-FeSV) encoding its primary translation product, p70gag-fgr, has been determined. From the nucleotide sequence, the amino acid sequence of this transforming protein was deduced. Computer analysis indicates that a portion of P70gag-fgr has extensive amino acid sequence homology with actin, a eukaryotic cytoskeletal protein. A second region of P70gag-fgr is closely related to the tyrosine-specific kinase gene family. Thus, the v-fgr oncogene appears to have arisen as a result of recombinational events involving two distinct cellular genes, one coding for a structural protein and the other for a protein kinase.

• Reed J, Kinzel V
• Near- and far-ultraviolet circular dichroism of the catalytic subunit of adenosine cyclic 5'-monophosphate dependent protein kinase.
• Biochemistry. 1984; 23: 1357-62
• Display abstract

• The circular dichroism spectrum of the catalytic subunit of cAMP-dependent protein kinase was measured in the far-UV (190-240 nm) and near-UV (250-300 nm) region. Data from the far-UV spectra were processed with the CONTIN program for estimation of globular protein secondary structure [ Provencher , S. W. (1982) CONTIN (Version 2) User's Manual, European Molecular Biology Laboratory, Heidelberg, West Germany]. The composition of the protein determined by this method was 49 +/- 2% alpha-helix, 20 +/- 4% beta-sheet, and 31 +/- 3% remainder. This composition changes when the protein is allowed to bind Kemptide , a synthetic peptide substrate, with more than half of the disordered portion of the protein taking the form of beta-sheet. A certain portion of the alpha-helical structure also appears to move into a beta-sheet form. The near-UV CD spectrum of catalytic subunit shows changes in aromatic amino acid dichroism associated with substrate binding. These changes can be ascribed with a fair degree of certainty to alterations in the orientation of a tyrosine residue at the surface of the protein. These findings are discussed in terms of previous work on induced dichroism in this enzyme with regard to control mechanisms operating at the active site.

• Takio K, Wade RD, Smith SB, Krebs EG, Walsh KA, Titani K
• Guanosine cyclic 3',5'-phosphate dependent protein kinase, a chimeric protein homologous with two separate protein families.
• Biochemistry. 1984; 23: 4207-18
• Display abstract

• The amino acid sequence of bovine lung cGMP-dependent protein kinase has been determined by degradation and alignment of two primary overlapping sets of peptides generated by cleavage at methionyl or arginyl residues. The protein contains 670 residues in a single N alpha-acetylated chain corresponding to a molecular weight of 76 331. The function of the molecule is considered in six segments of sequence which may correspond to four folding domains. From the amino terminus, the first segment is related to the dimerizing property of the protein. The second and third segments appear to have evolved from an ancestral tandem internal gene duplication, generating twin cGMP-binding domains which are homologous to twin domains in the regulatory subunits of cAMP-dependent protein kinase and to the cAMP-binding domain of the catabolite gene activator of Escherichia coli. The fourth and fifth segments may comprise one domain which is homologous to the catalytic subunits of cAMP-dependent protein kinase, of calcium-dependent phosphorylase b kinase, and of certain oncogenic viral protein tyrosine kinases. The regulatory, amino-terminal half of cGMP-dependent protein kinase appears to be related to a family of smaller proteins that bind cAMP for diverse purposes, whereas the catalytic, carboxyl-terminal half is related to a family of protein kinases of varying specificity and varying sensitivity to regulators. These data suggest that ancestral gene splicing events may have been involved in the fusion of two families of proteins to generate the allosteric character of this chimeric enzyme.

• Braun S, Abdel Ghany M, Racker E
• A rapid assay for protein kinases phosphorylating small polypeptides and other substrates.
• Anal Biochem. 1983; 135: 369-78
• Display abstract

• A new and rapid method of protein kinase assay is presented which is suitable for low-molecular-weight substrates, irrespective of their electrophoretic or chromatographic mobility. It depends on the phosphorylation of the substrates with [gamma-32P]ATP, hydrolysis of the pyrophosphate bonds by boiling in 1 N HCl, extraction of 32P with isobutanol-benzene, and measurement of the radioactivity of 32P-labeled phosphoesters in the water phase. The method is shown to be suitable for both tyrosine- and serine-phosphorylating protein kinases.

• Mayer JE, Schweiger M
• RNase III is positively regulated by T7 protein kinase.
• J Biol Chem. 1983; 258: 5340-3
• Display abstract

• RNase III activity of Escherichia coli is stimulated 4-fold after infection with bacterial virus T7. The mechanism of stimulation is based on phosphate transfer to RNase III by the T7 coded protein kinase. In vitro synthesized protein kinase also stimulates RNase III. Serine is the phosphate acceptor.

• Solomoniia RO, Nesterova MV, Severin ES
• [Physico-chemical properties of cyclic nucleotide-independent protein kinase from the myxomycete Physarum polycephalum]
• Biokhimiia. 1982; 47: 1552-5
• Display abstract

• Some physico-chemical properties of cyclic nucleotide-independent protein kinase from the myxomycete Physarum polycephalum were studied. The enzyme is not activated by Ca2+ and double-stranded RNA of poly(A)-poly(Y). The nature of the amino acid, target for phosphorylation, for the homogenous enzyme was established by two-dimensional electrophoresis, using casein as a protein substrate. The enzyme exclusively phosphorylates threonine residues in the casein molecule.

• Farron-Furstenthal F
• A one-step procedure for the determination of protein kinase activities and a protein kinase inhibitor in nuclear extract.
• Anal Biochem. 1980; 109: 203-6

• Baydoun H, Hoppe J, Jacob G, Wagner KG
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