Secondary literature sources for the UDPG_MGDP_dh_C domain

For each of the hand selected primary papers associated with the UDPG_MGDP_dh_C domain, 100 neighbouring papers are retrieved from PubMed. If one of these neighbouring papers is referenced by more than two primary papers, it is shown in the table below.

Purification and specificity of beta1,2-xylosyltransferase, an enzyme that contributes to the allergenicity of some plant proteins.

Zeng Y, Bannon G, Thomas VH, Rice K, Drake R, Elbein A
J Biol Chem. 1997; 272: 31340-7

The enzyme that transfers D-xylose from UDP-xylose to the beta-linked mannose of plant N-linked oligosaccharides was purified about 51,000-fold to apparent homogeneity from soybean microsomes. On SDS gels, two proteins of 56 and 59 kDa were detected and both were labeled to the same extent by the photoaffinity label, 5-N3-UDP-[32P]xylose. Labeling of both proteins was inhibited by cold UDP-xylose, but not by UDP-glucose. The amount of 5-N3-UDP-[32P]xylose that bound to the two protein bands was greatly increased in the presence of oligosaccharide acceptors. The best acceptor for xylose transfer and for stimulation of UDP-xylose binding was GlcNAc2Man3GlcNAc2-T, but GlcNAc1Man3GlcNAc2, with the GlcNAc on the 3-branch, was also a good acceptor and a good stimulator. A number of other N-linked oligosaccharides were poor acceptors, especially those with galactose units at the nonreducing termini. Many of the properties of this enzyme have been described, and the product of the reaction of UDP-xylose and GlcNAc2Man3(GlcNAc)2 was characterized as GlcNAcbeta1, 2Manalpha1, 6(GlcNAcbeta1,2Manalpha1,3)(Xylbeta1,2)Manbeta1, 4GlcNA c2-T by chemical and NMR methods.

Steady-state kinetic mechanism and reductive half-reaction of D-arginine dehydrogenase from Pseudomonas aeruginosa.

Yuan H, Fu G, Brooks PT, Weber I, Gadda G
Biochemistry. 2010; 49: 9542-50

D-arginine dehydrogenase from Pseudomonas aeruginosa catalyzes the oxidation of D-arginine to iminoarginine, which is hydrolyzed in solution to ketoarginine and ammonia. In the present study, we have genetically engineered an untagged form of the enzyme that was purified to high levels and characterized in its kinetic properties. The enzyme is a true dehydrogenase that does not react with molecular oxygen. Steady-state kinetic studies with D-arginine or D-histidine as substrate and PMS as the electron acceptor established a ping-pong bi-bi kinetic mechanism. With the fast substrate D-arginine a dead-end complex of the reduced enzyme and the substrate occurs at high concentrations of D-arginine yielding substrate inhibition, while the overall turnover is partially limited by the release of the iminoarginine product. With the slow substrate D-histidine the initial Michaelis complex undergoes an isomerization involving multiple conformations that are not all equally catalytically competent for the subsequent oxidation reaction, while the overall turnover is at least partially limited by flavin reduction. The kinetic data are interpreted in view of the high-resolution crystal structures of the iminoarginine--and iminohistidine--enzyme complexes.

Purification and characterization of phosphomannomutase/phosphoglucomutase from Pseudomonas aeruginosa involved in biosynthesis of both alginate and lipopolysaccharide.

Ye RW, Zielinski NA, Chakrabarty AM
J Bacteriol. 1994; 176: 4851-7

The algC gene from Pseudomonas aeruginosa has been shown to encode phosphomannomutase (PMM), an essential enzyme for biosynthesis of alginate and lipopolysaccharide (LPS). This gene was overexpressed under control of the tac promoter, and the enzyme was purified and its substrate specificity and metal ion effects were characterized. The enzyme was determined to be a monomer with a molecular mass of 50 kDa. The enzyme catalyzed the interconversion of mannose 1-phosphate (M1P) and mannose 6-phosphate, as well as that of glucose 1-phosphate (G1P) and glucose 6-phosphate. The apparent Km values for M1P and G1P were 17 and 22 microM, respectively. On the basis of Kcat/Km ratio, the catalytic efficiency for G1P was about twofold higher than that for M1P. PMM also catalyzed the conversion of ribose 1-phosphate and 2-deoxyglucose 6-phosphate to their corresponding isomers, although activities were much lower. Purified PMM/phosphoglucomutase (PGM) required Mg2+ for maximum activity; Mn2+ was the only other divalent metal that showed some activation. The presence of other divalent metals in addition to Mg2+ in the reaction inhibited the enzymatic activity. PMM and PGM activities could not be detected in nonmucoid algC mutant strain 8858 and in LPS-rough algC mutant strain AK1012, while they were present in the wild-type strains as well as in algC-complemented mutant strains. This evidence suggests that AlgC functions as PMM and PGM in vivo, converting phosphomannose and phosphoglucose in the biosynthesis of both alginate and LPS.

Involvement of the alginate algT gene and integration host factor in the regulation of the Pseudomonas aeruginosa algB gene.

Wozniak DJ, Ohman DE
J Bacteriol. 1993; 175: 4145-53

Strains of Pseudomonas aeruginosa causing pulmonary infection in cystic fibrosis patients are often mucoid because of the synthesis of a capsular polysaccharide called alginate. Regulation of alginate biosynthesis includes the algB gene product (AlgB), which belongs to a class of proteins that control gene transcription in response to environmental stimuli. In this study, a homolog of the DNA-binding-and-bending protein integration host factor (IHF) and the positive regulatory gene algT were shown to be involved in algB expression. An algB-cat gene fusion was constructed on a low-copy-number, broad-host-range plasmid. In alginate-producing (Alg+) P. aeruginosa, levels of chloramphenicol acetyltransferase from algB-cat were twofold higher than in spontaneous Alg- or algT::Tn501 mutant strains, indicating that the mucoid status of the cell influences algB transcription. An algB transcription initiation site was identified 286 nucleotides upstream of translation initiation and revealed an Escherichia coli sigma 70-like promoter. Sequences in the algB promoter region were highly similar to the consensus E. coli IHF binding site. In DNA gel band mobility shift assays, a protein present in extracts from IHF+ E. coli strains and IHF purified from E. coli bound specifically to these algB DNA fragments, while extracts prepared from isogenic IHF- E. coli strains failed to alter the mobility of algB DNA fragments containing the consensus IHF binding site. A protein in cell extracts prepared from P. aeruginosa strains also demonstrated binding to algB fragments containing the IHF binding site, and the position of the complex formed with these extracts was identical to that of the complex formed with purified IHF. Moreover, this binding could be inhibited by anti-IHF antibodies. To test the role of the IHF site in algB regulation, site-specific mutations in the algB IHF site, based on changes which severely affect IHF binding in E. coli, were generated. When either purified E. coli IHF or extracts from P. aeruginosa were used in DNA binding studies, the algB mutant DNAs were severely reduced in IHF binding. Mutations affecting IHF binding at the algB promoter were introduced into the algB-cat plasmid, and all resulted in severely impaired transcriptional activity in Alg- and algT mutant strains of P. aeruginosa. However, these mutations resulted in similar or slightly reduced algB-cat transcription in Alg+ and algB::Tn501 mutant strains. Thus, the algT product plays a positive role in the high-level expression of algB in mucoid cells, whereas as protein present in P.aeruginosa extracts which is likely an IHF homolog plays a positive role in maintaining a basal level of algB expression in nonmucoid strains.

Comparison of surface fibroblastic cells in subcutaneous air pouch and synovial lining: differences in uridine diphosphoglucose dehydrogenase activity.

Wilkinson LS, Moore AR, Pitsillides AA, Willoughby DA, Edwards JC
Int J Exp Pathol. 1993; 74: 113-5

In contrast to synovial tissue, rat subcutaneous air pouch lining was found to lack cells showing high activity of uridine diphosphoglucose dehydrogenase, an enzyme involved in hyaluronan synthesis. This indicates that the properties of cells on the surface of synovium are not determined simply by tissue cavitation. Shearing forces may be more important in inducing the specialized behaviour of synovial surface fibroblasts.

Identification, properties and genetic control of UDP-glucose: isovitexin 7-O-glucosyltransferase isolated from petals of Melandrium album.

van Brederode J, van Nigtevecht G
Mol Gen Genet. 1973; 122: 215-29

Purification and some properties of L-fucose dehydrogenase from Agrobacterium radiobacter and its application to the assay of bound-fucose in glycoconjugates.

Tsuji Y, Koike A, Yamamoto K, Tochikura T
Biochim Biophys Acta. 1992; 1117: 167-73

L-Fucose dehydrogenase was found in the cell extract of Agrobacterium radiobacter and purified to homogeneity about 480-fold with 16% recovery. The molecular weight of the enzyme was approx. 64,000. The enzyme was active in the neutral pH range, unlike other L-fucose or D-arabinose dehydrogenases which are active only in the alkaline pH range. Using this enzyme and alpha-L-fucosidase F-I of Bacillus circulans (Tsuji, Y., Yamamoto, K., Tochikura, T., Seno, T., Ohkubo, Y. and Yamaguchi, H. (1990) J. Biochem. 107, 324-330) simultaneously, we developed a new coupled enzymatic method in a single buffer system for determining bound-fucose in biological materials. The fucose released by alpha-L-fucosidase F-I was oxidized with L-fucose dehydrogenase in the presence of NAD+, and the NADH formed was measured by absorbance of ultraviolet or utilized to generate color in a reaction involving CuSO4 and neocuproine. Using these methods, bound-fucose in various oligosaccharides and proteins such as lacto-N-fucopentaoses and porcine gastric mucin were quantitated within 15 min.

Identification of two cysteine residues involved in the binding of UDP-GalNAc to UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1).

Tenno M, Toba S, Kezdy FJ, Elhammer AP, Kurosaka A
Eur J Biochem. 2002; 269: 4308-16

Biosynthesis of mucin-type O-glycans is initiated by a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases, which contain several conserved cysteine residues among the isozymes. We found that a cysteine-specific reagent, p-chloromercuriphenylsulfonic acid (PCMPS), irreversibly inhibited one of the isozymes (GalNAc-T1). Presence of either UDP-GalNAc or UDP during PCMPS treatment protected GalNAc-T1 from inactivation, to the same extent. This suggests that GalNAc-T1 contains free cysteine residues interacting with the UDP moiety of the sugar donor. For the functional analysis of the cysteine residues, several conserved cysteine residues in GalNAc-T1 were mutated individually to alanine. All of the mutations except one resulted in complete inactivation or a drastic decrease in the activity, of the enzyme. We identified only Cys212 and Cys214, among the conserved cysteine residues in GalNAc-T1, as free cysteine residues, by cysteine-specific labeling of GalNAc-T1. To investigate the role of these two cysteine residues, we generated cysteine to serine mutants (C212S and C214S). The serine mutants were more active than the corresponding alanine mutants (C212A and C214A). Kinetic analysis demonstrated that the affinity of the serine-mutants for UDP-GalNAc was decreased, as compared to the wild type enzyme. The affinity for the acceptor apomucin, on the other hand, was essentially unaffected. The functional importance of the introduced serine residues was further demonstrated by the inhibition of all serine mutant enzymes with diisopropyl fluorophosphate. In addition, the serine mutants were more resistant to modification by PCMPS. Our results indicate that Cys212 and Cys214 are sites of PCMPS modification, and that these cysteine residues are involved in the interaction with the UDP moiety of UDP-GalNAc.

Characterization of human UDP-glucose dehydrogenase. CYS-276 is required for the second of two successive oxidations.

Sommer BJ, Barycki JJ, Simpson MA
J Biol Chem. 2004; 279: 23590-6

UDP-glucose dehydrogenase (UGDH) catalyzes two oxidations of UDP-glucose to yield UDP-glucuronic acid. Pathological overproduction of extracellular matrix components may be linked to the availability of UDP-glucuronic acid; therefore UGDH is an intriguing therapeutic target. Specific inhibition of human UGDH requires detailed knowledge of its catalytic mechanism, which has not been characterized. In this report, we have cloned, expressed, and affinity-purified the human enzyme and determined its steady state kinetic parameters. The human enzyme is active as a hexamer with values for Km and Vmax that agree well with those reported for a bovine homolog. We used crystal coordinates for Streptococcus pyogenes UGDH in complex with NAD+ cofactor and UDP-glucose substrate to generate a model of the enzyme active site. Based on this model, we selected Cys-276 and Lys-279 as likely catalytic residues and converted them to serine and alanine, respectively. Enzymatic activity of C276S and K279A point mutants was not measurable under normal assay conditions. Rate constants measured over several hours demonstrated that K279A continued to turn over, although 250-fold more slowly than wild type enzyme. C276S, however, performed only a single round of oxidation, indicating that it is essential for the second oxidation. This result is consistent with the postulated role of Cys-276 as a catalytic residue and supports its position in the reaction mechanism for the human enzyme. Lys-279 is likely to have a role in positioning active site residues and in maintaining the hexameric quaternary structure.

Crystal structure of GDP-mannose dehydrogenase: a key enzyme of alginate biosynthesis in P. aeruginosa.

Snook CF, Tipton PA, Beamer LJ
Biochemistry. 2003; 42: 4658-68

The enzyme GMD from Pseudomonas aeruginosa catalyzes the committed step in the synthesis of the exopolysaccharide alginate. Alginate is a major component of P. aeruginosa biofilms that protect the bacteria from the host immune response and antibiotic therapy. The 1.55 A crystal structure of GMD in ternary complex with its cofactor NAD(H) and product GDP-mannuronic acid reveals that the enzyme forms a domain-swapped dimer with two polypeptide chains contributing to each active site. The extensive dimer interface provides multiple opportunities for intersubunit communication. Comparison of the GMD structure with that of UDP-glucose dehydrogenase reveals the structural basis of sugar binding specificity that distinguishes these two related enzyme families. The high-resolution structure of GMD provides detailed information on the active site of the enzyme and a template for structure-based inhibitor design.

The algD promoter: regulation of alginate production by Pseudomonas aeruginosa in cystic fibrosis.

Schurr MJ, Martin DW, Mudd MH, Hibler NS, Boucher JC, Deretic V
Cell Mol Biol Res. 1993; 39: 371-6

Pseudomonas aeruginosa mutants that overproduce the exopolysaccharide alginate and assume mucoid phenotype are associated with the establishment of chronic respiratory disease in cystic fibrosis. The initially invading strains are nonmucoid and frequently convert into the mucoid form. Mucoidy is regulated at the transcriptional level, mainly at the promoter of the algD gene. Control of the algD promoter represents a cooperative effort of several types of regulatory elements including bacterial signal transduction factors (principally through the response regulator AlgR) and histone like elements (e.g., Hp1 and possibly IHF). Our more recent studies have shown that conversion to mucoidy is a result of mutations in the muc genes within the algU-mucA-mucB cluster. The algU gene encodes a protein that resembles Spo0H, a sigma factor from Bacillus subtilis, which controls development of sporulation and competence. The mucA and mucB genes appear to control the activity of AlgU. Frameshift mutations that inactivate these proteins result in a strong transcriptional activation of algD, and conversion to mucoidy in both laboratory and clinical strains of P. aeruginosa.

Gene cluster controlling conversion to alginate-overproducing phenotype in Pseudomonas aeruginosa: functional analysis in a heterologous host and role in the instability of mucoidy.

Schurr MJ, Martin DW, Mudd MH, Deretic V
J Bacteriol. 1994; 176: 3375-82

Conversion to mucoidy, caused by the overproduction of the exopolysaccharide alginate in laboratory and cystic fibrosis strains of Pseudomonas aeruginosa, can occur via frameshift or nonsense mutations in the second gene of the algU mucA mucB cluster. The first gene of the cluster, algU, encodes a putative alternative sigma factor required for algD transcription. The algD gene encodes a critical alginate biosynthetic enzyme and is invariably activated in mucoid P. aeruginosa cells. To investigate the function of the genes controlling conversion to mucoidy, the wild-type algU mucA mucB cluster from the standard genetic strain PAO1 was used to reconstitute algD transcription in Escherichia coli. Transcription of an algD-lacZ chromosomal fusion in E. coli was detected upon introduction of plasmid-borne algU mucA mucB. Moreover, insertional inactivation of either mucA or mucB resulted in further stimulation of transcriptional activity from the algD promoter. This activation was dependent on algU, since a double algU mucA mutation abrogated transcription of algD. These experiments suggest that the phenotypic manifestations of muc mutations, i.e., increased algD expression and mucoid phenotype, depend on the presence of an active algU gene and that this regulator and the factors encoded by the downstream genes interact. Further support for these conclusions came from the investigations of the mechanism of reversion to nonmucoidy in P. aeruginosa, a phenomenon frequently referred to as the instability of mucoid phenotype. Spontaneous nonmucoid derivatives of the mucoid strain PAO578 carrying the mucA22 mutation were examined for the presence of alterations within the algU mucA mucB locus. Point mutations which inactivated algU were detected in some, but not all, nonmucoid revertants. No reversion of the original mucA22 mutation (a deletion of one C) was observed in any of the investigated strains. This observation suggests that the process of conversion to nonmucoidy ban be explained, at least partially, by second-site suppressor mutations and that a fraction of such mutations occurs in algU.

[Alginates of Pseudomonas aeruginosa: a complex regulation of the pathway of biosynthesis].

Schmitt-Andrieu L, Hulen C
C R Acad Sci III. 1996; 319: 153-60

Pseudomonas aeruginosa is an opportunistic pathogen causing severe infections, especially in lungs of patients with cystic fibrosis. Environmental conditions induce the production by the bacteria of a viscous mucoid exopolysaccharide, called alginate, which is one of the most important factor of virulence of P. aeruginosa. Alginate is a linear polymer of beta-1, 4-linked L-guluronic acid and D-mannuronic acid. The alginate biosynthetic pathway involves genes called alg which are clustered at the 34 min region of chromosomal DNA of P. aeruginosa. The key enzyme of alginate biosynthesis, the GDP-mannose dehydrogenase is encoded by the gene algD. Expression of algD is positively controlled by several proteins, especially AlgU, a putative sigma factor homologous to sigma E of E. coli, AlgR and AlgP, a transactivator and an histone-like respectively. Here, a scheme of alginate biosynthetic pathway and a model for the alg genes regulation are described from results published in literature and from our own interpretation.

Regulatory properties of purified 3-phosphoglycerate dehydrogenase from Bacillus subtilis.

Saski R, Pizer LI
Eur J Biochem. 1975; 51: 415-27

3-Phosphoglycerate dehydrogenase (3-phosphoglycerate:NAD oxidoreductase, EC. 1.1.1.95) was purified from Bacillus subtilis by conventional methods. The final preparation was homogeneous by electrophoretic analysis and had a sedimentation constant of 6.3 S. On the basis of gel filtration data the enzyme had a molecular weight of about 166000. The plot of velocity versus phosphoglycerate concentration was biphasic while similar plots for hydroxypyruvate phosphate and NADH were the conventional hyperbolic type. The enzyme was specifically inhibited by serine. The inhibition was time dependent, requiring several minutes incubation before a constant level of inhibition was achieved. Serine inhibition was of the "mixed type" with respect to 3-phosphoglycerate and Hill plots of these data had slopes that approached 2. Desensitization of the enzyme to serine inhibition was achieved by incubation in the absence of dithiothreitol. The desensitized enzyme was different from the native enzyme in fluoresence properties, sedimentation characteristics and in the absence of the biphasic phosphoglycerate saturation curve. Evidence was obtained for the participation of sulphydryl groups in the changes in protein structure responsible for serine inhibition as well as the dehydrogenase activity of the enzyme.

The presence of elements of a dinucleotide fold in UDP-glucose 4-epimerase from Saccharomyces fragilis.

Samanta AK, Bhaduri A
Biochim Biophys Acta. 1982; 707: 129-32

UDPglucose 4-epimerase (EC 5.1.3.2) from Saccharomyces fragilis is a holoenzyme containing 1 mol NAD per mol dimeric protein. The enzyme can be dissociated with p-chloromercuribenzoate and can be reconstituted in the presence of 2-mercaptoethanol and exogenous NAD. Using Cibacron blue F3GA in this reconstituting system, competition between NAD and the dye for the pyridine nucleotide-binding site could be demonstrated. Inactive holoenzyme containing Cibacron blue can also be obtained under these conditions. These data suggest the possible presence of elements of a dinucleotide fold in this enzyme.

Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants.

Rosano C, Bisso A, Izzo G, Tonetti M, Sturla L, De Flora A, Bolognesi M
J Mol Biol. 2000; 303: 77-91

GDP-4-keto-6-deoxy-d-mannose epimerase/reductase is a bifunctional enzyme responsible for the last step in the biosynthesis of GDP-l-fucose, the substrate of fucosyl transferases. Several cell-surface antigens, including the leukocyte Lewis system and cell-surface antigens in pathogenic bacteria, depend on the availability of GDP-l-fucose for their expression. Therefore, the enzyme is a potential target for therapy in pathological states depending on selectin-mediated cell-to-cell interactions. Previous crystallographic investigations have shown that GDP-4-keto-6-deoxy-d-mannose epimerase/reductase belongs to the short-chain dehydrogenase/reductase protein homology family. The enzyme active-site region is at the interface of an N-terminal NADPH-binding domain and a C-terminal domain, held to bind the substrate. The design, expression and functional characterization of seven site-specific mutant forms of GDP-4-keto-6-deoxy-d-mannose epimerase/reductase are reported here. In parallel, the crystal structures of the native holoenzyme and of three mutants (Ser107Ala, Tyr136Glu and Lys140Arg) have been investigated and refined at 1. 45-1.60 A resolution, based on synchrotron data (R-factors range between 12.6 % and 13.9 %). The refined protein models show that besides the active-site residues Ser107, Tyr136 and Lys140, whose mutations impair the overall enzymatic activity and may affect the coenzyme binding mode, side-chains capable of proton exchange, located around the expected substrate (GDP-4-keto-6-deoxy-d-mannose) binding pocket, are selectively required during the epimerization and reduction steps. Among these, Cys109 and His179 may play a primary role in proton exchange between the enzyme and the epimerization catalytic intermediates. Finally, the additional role of mutated active-site residues involved in substrate recognition and in enzyme stability has been analyzed.

Overexpression of UDP-glucose dehydrogenase in Escherichia coli results in decreased biosynthesis of K5 polysaccharide.

Roman E, Roberts I, Lidholt K, Kusche-Gullberg M
Biochem J. 2003; 374: 767-72

The Escherichia coli K5 capsular polysaccharide (glycosaminoglycan) chains are composed of the repeated disaccharide structure: -GlcAbeta1,4-GlcNAcalpha1,4-(where GlcA is glucuronic acid and GlcNAc is N-acetyl-D-glucosamine). The GlcA, present in most glycosaminoglycans, is donated from UDP-GlcA, which, in turn, is generated from UDP-glucose by the enzyme UDP-glucose dehydrogenase (UDPGDH). The formation of UDP-GlcA is critical for the biosynthesis of glycosaminoglycans. To investigate the role of UDPGDH in glycosaminoglycan biosynthesis, we used K5 polysaccharide biosynthesis as a model. E. coli was transformed with the complete gene cluster for K5 polysaccharide production. Additional transformation with an extra copy of UDPGDH resulted in an approx. 15-fold increase in the in vitro UDPGDH enzyme activity compared with the strain lacking extra UDPGDH. UDP-GlcA levels were increased 3-fold in overexpressing strains. However, metabolic labelling with [14C]glucose showed, unexpectedly, that overexpression of UDPGDH lead to decreased formation of K5 polysaccharide. No significant difference in the K5 polysaccharide chain length was observed between control and overexpressing strains, indicating that the decrease in K5-polysaccharide production most probably was due to synthesis of fewer chains. Our results suggest that K5-polysaccharide biosynthesis is strictly regulated such that increasing the amount of available UDP-GlcA results in diminished K5-polysaccharide production.

Uridine diphosphate glucose synthase from calf liver: determinants of enzyme activity in vitro.

Roach PJ, Warren KR, Atkinson DE
Biochemistry. 1975; 14: 5445-50

The reaction catalyzed by calf liver uridine diphosphate glucose synthase (pyrophosphorylase) (EC 2.7.7.9; UTP + glucose 1-phosphate = UDP-glucose + PPi) is an example of an enzymic reaction in which a nucleoside triphosphate other than ATP is the immediate source of metabolic energy. Kinetic properties of the enzyme, acting in the direction of UCP-glucose formation were investigated in vitro. The reaction was inhibited by UDP-glucose (0.072), Pi (11), UDP (1.6), UDP-xylose (0.87), UDP-glucuronate (1.3), and UDP-galacturonate (0.95). The numbers in parentheses indicate the concentration (mM) required for half-maximal inhibition under the conditions used. Other compounds tested, including ATP, ADP, and AMP, had no effect. Over a range of concentrations of UTP (0.04-0.8 MM) and UDP-glucose (0.05-0.03 mM), the reaction rate was more dependent on the concentration ratio [UDP-glucose]/[UTP] than on the absolute concentration of either compound. Comparison of the kinetic properties in vitro with estimates of metabolite levels in vivo suggests that (1) the enzyme operates in a range far from its maximal rate, and (2) the concentrations of glucose 1-phosphate and Pi and the ratio [UDP-glucose]/[UTP] may be the most important determinants of UDP-glucose synthase activity.

Insights into the assembly of the alginate biosynthesis machinery in Pseudomonas aeruginosa.

Rehman ZU, Wang Y, Moradali MF, Hay ID, Rehm BH
Appl Environ Microbiol. 2013; 79: 3264-72

Pseudomonas aeruginosa is an opportunistic pathogen of particular significance to cystic fibrosis patients. This bacterium produces the exopolysaccharide alginate, which is an indicator of poor prognosis for these patients. The proteins required for alginate polymerization and secretion are encoded by genes organized in a single operon; however, the existence of internal promoters has been reported. It has been proposed that these proteins form a multiprotein complex which extends from the inner to outer membrane. Here, experimental evidence supporting such a multiprotein complex was obtained via mutual stability analysis, pulldown assays, and coimmunoprecipitation. The impact of the absence of single proteins or subunits on this multiprotein complex, i.e., on the stability of potentially interacting proteins, as well as on alginate production was investigated. Deletion of algK in an alginate-overproducing strain, PDO300, interfered with the polymerization of alginate, suggesting that in the absence of AlgK, the polymerase and copolymerase subunits, Alg8 and Alg44, are destabilized. Based on mutual stability analysis, interactions between AlgE (outer membrane), AlgK (periplasm), AlgX (periplasm), Alg44 (inner membrane), Alg8 (inner membrane), and AlgG (periplasm) were proposed. Coimmunoprecipitation using a FLAG-tagged variant of AlgE further demonstrated its interaction with AlgK. Pulldown assays using histidine-tagged AlgK showed that AlgK interacts with AlgX, which in turn was also copurified with histidine-tagged Alg44. Detection of AlgG and AlgE in PAO1 supported the existence of internal promoters controlling expression of the respective genes. Overall experimental evidence was provided for the existence of a multiprotein complex required for alginate polymerization and secretion.

Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa.

Raymond CK, Sims EH, Kas A, Spencer DH, Kutyavin TV, Ivey RG, Zhou Y, Kaul R, Clendenning JB, Olson MV
J Bacteriol. 2002; 184: 3614-22

The outer carbohydrate layer, or O antigen, of Pseudomonas aeruginosa varies markedly in different isolates of these bacteria, and at least 20 distinct O-antigen serotypes have been described. Previous studies have indicated that the major enzymes responsible for O-antigen synthesis are encoded in a cluster of genes that occupy a common genetic locus. We used targeted yeast recombinational cloning to isolate this locus from the 20 internationally recognized serotype strains. DNA sequencing of these isolated segments revealed that at least 11 highly divergent gene clusters occupy this region. Homology searches of the encoded protein products indicated that these gene clusters are likely to direct O-antigen biosynthesis. The O15 serotype strains lack functional gene clusters in the region analyzed, suggesting that O-antigen biosynthesis genes for this serotype are harbored in a different portion of the genome. The overall pattern underscores the plasticity of the P. aeruginosa genome, in which a specific site in a well-conserved genomic region can be occupied by any of numerous islands of functionally related DNA with diverse sequences.

Fluorescence properties of reconstituted forms of UDP-glucose 4-epimerase from Saccharomyces fragilis.

Ray M, Bhaduri A
J Biol Chem. 1980; 255: 10782-86

UDP-glucose 4-epimerase from Saccharomyces fragilis exhibits a very characteristic intense fluorescence with an excitation maximum at 360 nm and an emission maximum at 433 nm. The fluorescence spectrum resembles the fluorescence of free NADH with an apparent blue shift and, although the exact nature of the fluorophore is not known, the protein-bound NAD, which is a coenzyme for this reaction, or its reduced form is obviously involved in the emission of the fluorescence. The fluorphore therefore constitutes part of the active site. The inactivation of epimerase with diazinedicarboxylic acid bis(N,N-diethylamide), a reaction shown in the previous paper to form a disulfide linkage across the subunits, results in a simultaneous and correlated loss of the characteristic fluorescence of the enzyme. Reaction with mercaptoethanol restores the native fluorescence with a 2 nm blue shift in emission maximum. These epxeriments provide additional evidence that the two conformationally vicinal sulfhydryl groups are located at the active site. Unlike the reconstituted enzyme obtained from the diamide-inactivated enzyme, the partialy active enzymes reconstituted from p-chloromercuribenzoate-inactivated and heat-inactivated enzymes fail to show the reappearance of the characteristic native fluorescence. Treatment with N-ethylmaleamide, on the other hand, leads to a form of the inactive enzyme that fully retains its fluorescent properties. A model depicting the minimal changes at the active site during the process of inactivation and reconstitution by these various treatments is presented.

UDP glucose-4 epimerase from Saccharomyces fragilis: interaction with sugar phosphates at an effector site.

Ray M, Bhaduri A
Biochem Biophys Res Commun. 1974; 60: 1081-9

Presence of two conformationally vicinal sulfhydryl groups at the active site of UDP-glucose 4-epimerase from Saccharomyces fragilis.

Ray M, Bhaduri A
J Biol Chem. 1980; 255: 10777-81

UDP-glucose 4-epimerase from Saccharomyces fragilis was inactivated by diazene dicarboxylic acid bis-N,N-dimethylamide or diamide, a compound that can specifically oxidize conformationally vicinal sulfhydryl groups on protein surfaces. The inactive enzyme was shown to retain the original dimeric structure and NAD, which is a coenzyme for this reaction, was not dissociated from the apoenzyme. The loss of activity was due to the direct modification of sulfhydryl groups and could not be attributed to any subsequent loss of structural integrity. The activity of the enzyme could be regained almost completely on incubation with mercaptoethanol alone and no exogenous NAD was needed for reactivation. The reactivated enzyme showed most of the characteristic properties of the native enzyme like activation by cations or inhibition by UMP. Presence of substrate provided partial protection against inactivation by the reagent. Formation of disulfide bond(s) across the subunits was demonstrated by sodium dodecyl sulfate gel electrophoresis in absence of mercaptoethanol. Titration of native and diamide-inactivated enzyme with p-chloromercuribenzoate revealed that only two sulfhydryl groups were involved in the formation of the disulfide cross-linkage across the subunits. The above results indicate the possible presence of two conformationally vicinal sulfhydryl groups at two different subunits of the enzyme that constitute part of the active site.

Cloning and expression studies of the Dunaliella salina UDP-glucose dehydrogenase cDNA.

Qinghua H, Dairong Q, Qinglian Z, Shunji H, Yin L, Linhan B, Zhirong Y, Yi C
DNA Seq. 2005; 16: 202-6

The enzyme UDP-glucose dehydrogenase (EC 1.1.1.22) converts UDP-glucose to UDP-glucuronate. Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of primary cell walls. A cDNA, named DsUGDH, (GeneBank accession number: AY795899) corresponding to UGDH was cloned by RT-PCR approach from Dunaliella salina. The cDNA is 1941-bp long and has an open reading frame encoded a protein of 483 amino acids with a calculated molecular weight of 53 kDa. The derived amino acids sequence shows high homology with reported plants UGDHs, and has highly conserved amino acids motifs believed to be NAD binding site and catalytic site. Although UDP-glucose dehydrogenase is a comparatively well characterized enzyme, the cloning and characterization of the green alga Dunaliella salina UDP-glucose dehydrogenase gene is very important to understand the salt tolerance mechanism of Dunaliella salina. Northern analyses indicate that NaCl can induce the expression the DsUGDH.

Optical spectroscopy of nicotinoprotein alcohol dehydrogenase from Amycolatopsis methanolica: a comparison with horse liver alcohol dehydrogenase and UDP-galactose epimerase.

Piersma SR, Visser AJ, de Vries S, Duine JA
Biochemistry. 1998; 37: 3068-77

The NADH absorbance spectrum of nicotinoprotein (NADH-containing) alcohol dehydrogenase from Amycolatopsis methanolica has a maximum at 326 nm. Reduced enzyme-bound pyridine dinucleotide could be reversibly oxidized by acetaldehyde. The fluorescence excitation spectrum for NADH bound to the enzyme has a maximum at 325 nm. Upon excitation at 290 nm, energy transfer from tryptophan to enzyme-bound NADH was negligible. The fluorescence emission spectrum (excitation at 325 nm) for NADH bound to the enzyme has a maximum at 422 nm. The fluorescence intensity is enhanced by a factor of 3 upon binding of isobutyramide (Kd = 59 microM). Isobutyramide acts as competitive inhibitor (Ki = 46 microM) with respect to the electron acceptor NDMA (N,N-dimethyl-p-nitrosoaniline), which binds to the enzyme containing the reduced cofactor. The nonreactive substrate analogue trifluoroethanol acts as a competitive inhibitor with respect to the substrate ethanol (Ki = 1.6 microM), which binds to the enzyme containing the oxidized cofactor. Far-UV circular dichroism spectra of the enzyme containing NADH and the enzyme containing NAD+ were identical, indicating that no major conformational changes occur upon oxidation or reduction of the cofactor. Near-UV circular dichroism spectra of NADH bound to the enzyme have a minimum at 323 nm (Deltaepsilon = -8.6 M-1 cm-1). The fluorescence anisotropy decay of enzyme-bound NADH showed no rotational freedom of the NADH cofactor. This implies a rigid environment as well as lack of motion of the fluorophore. The average fluorescence lifetime of NADH bound to the enzyme is 0.29 ns at 20 degreesC and could be resolved into at least three components (in the range 0.13-0.96 ns). Upon binding of isobutyramide to the enzyme-containing NADH, the average excited-state lifetime increased to 1.02 ns and could be resolved into two components (0.37 and 1.11 ns). The optical spectra of NADH bound to nicotinoprotein alcohol dehydrogenase have blue-shifted maxima compared to other NADH-dehydrogenase complexes, but comparable to that observed for NADH bound to horse liver alcohol dehydrogenase. The fluorescence lifetime of NADH bound to the nicotinoprotein is very short compared to enzyme-bound NADH complexes, also compared to NADH bound to horse liver alcohol dehydrogenase. The cofactor-protein interaction in the nicotinoprotein alcohol dehydrogenase active site is more rigid and apolar than that in horse liver alcohol dehydrogenase. The optical properties of NADH bound to nicotinoprotein alcohol dehydrogenase differ considerably from NADH (tightly) bound to UDP-galactose epimerase from Escherichia coli. This indicates that although both enzymes have NAD(H) as nonexchangeable cofactor, the NADH binding sites are quite different.

Purification and characterization of an active fragment of the LasA protein from Pseudomonas aeruginosa: enhancement of elastase activity.

Peters JE, Galloway DR
J Bacteriol. 1990; 172: 2236-40

A 22-kilodalton protein purified from the culture supernatant fraction of Pseudomonas aeruginosa (strains PA220 and PAO1) was found to enhance the elastolytic activity of purified P. aeruginosa elastase. N-terminal sequence analysis identified the protein as a fragment of the lasA gene product (P.A. Schad and B.H. Iglewski, J. Bacteriol. 170:2784-2789, 1988). However, comparative analysis with the reported LasA sequence indicated that the purified LasA fragment is longer than the deduced sequence reported. The purified LasA fragment had minimal elastolytic and proteolytic activity and did not enhance the proteolytic activity of purified elastase, yet enhanced the elastolytic activity more than 25-fold. The LasA fragment was found to also enhance the elastolytic activities of thermolysin, human neutrophil elastase, and proteinase K. The results presented here suggest that the LasA protein interacts with the elastin substrate rather than modifying elastase.

UDP-glucose dehydrogenase. Structural characteristics.

Perozich J, Leksana A, Hempel J
Adv Exp Med Biol. 1995; 372: 79-84

UDPglucose dehydrogenase. Kinetics and their mechanistic implications.

Ordman AB, Kirkwood S
Biochim Biophys Acta. 1977; 481: 25-32

Initial velocity and product inhibition studies were carried out on UDP-glucose dehydrogenase (UDPglucose: NAD+ 6-oxidoreductase, EC 1.1.1.22) from beef liver to determine if the kinetics of the reaction are compatible with the established mechanism. An intersecting initial velocity pattern was observed with NAD+ as the variable substrate and UDPG as the changing fixed substrate. UDPglucuronic acid gave competitive inhibition of UDPG and non-competitive inhibition of NAD+. Inhibition by NADH gave complex patterns.Lineweaver-Burk plots of 1/upsilon versus 1/NAD+ at varied levels of NADH gave highly non-linear curves. At levels of NAD+ below 0.05 mM, non-competitive inhibition patterns were observed giving parabolic curves. Extrapolation to saturation with NAD+ showed NADH gave linear uncompetitive inhibition of UDPG if NAD+ was saturating. However, at levels of NAD+ above 0.10 mM, NADH became a competitive inhibitor of NAD+ (parabolic curves) and when NAD+ was saturating NADH gave no inhibition of UDPG. NADH was non-competitive versus UDPG when NAD+ was not saturating. These results are compatible with a mechanism in which UDPG binds first, followed by NAD+, which is reduced and released. A second mol of NAD+ is then bound, reduced, and released. The irreversible step in the reaction must occur after the release of the second mol of NADH but before the release of UDPglucuronic acid. This is apparently caused by the hydrolysis of a thiol ester between UDPglucoronic acid and the essential thiol group of the enzyme. Examination of rate equations indicated that this hydrolysis is the rate-limiting step in the overall reaction. The discontinuity in the velocities observed at high NAD+ concentrations is apparently caused by the binding of NAD+ in the active site after the release of the second mol of NADH, eliminating the NADH inhibition when NAD+ becomes saturating.

Functional analysis of Arabidopsis thaliana RHM2/MUM4, a multidomain protein involved in UDP-D-glucose to UDP-L-rhamnose conversion.

Oka T, Nemoto T, Jigami Y
J Biol Chem. 2007; 282: 5389-403

UDP-L-rhamnose is required for the biosynthesis of cell wall rhamnogalacturonan-I, rhamnogalacturonan-II, and natural compounds in plants. It has been suggested that the RHM2/MUM4 gene is involved in conversion of UDP-D-glucose to UDP-L-rhamnose on the basis of its effect on rhamnogalacturonan-I-directed development in Arabidopsis thaliana. RHM2/MUM4-related genes, RHM1 and RHM3, can be found in the A. thaliana genome. Here we present direct evidence that all three RHM proteins have UDP-D-glucose 4,6-dehydratase, UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase, and UDP-4-keto-L-rhamnose 4-keto-reductase activities in the cytoplasm when expressed in the yeast Saccharomyces cerevisiae. Functional domain analysis revealed that the N-terminal region of RHM2 (RHM2-N; amino acids 1-370) has the first activity and the C-terminal region of RHM2 (RHM2-C; amino acids 371-667) has the two following activities. This suggests that RHM2 converts UDP-d-glucose to UDP-L-rhamnose via an UDP-4-keto-6-deoxy-D-glucose intermediate. Site-directed mutagenesis of RHM2 revealed that mucilage defects in MUM4-1 and MUM4-2 mutant seeds of A. thaliana are caused by abolishment of RHM2 enzymatic activity in the mutant strains and furthermore, that the GXXGXX(G/A) and YXXXK motifs are important for enzymatic activity. Moreover, a kinetic analysis of purified His(6)-tagged RHM2-N protein revealed 5.9-fold higher affinity of RHM2 for UDP-D-glucose than for dTDP-D-glucose, the preferred substrate for dTDP-D-glucose 4,6-dehydratase from bacteria. RHM2-N activity is strongly inhibited by UDP-L-rhamnose, UDP-D-xylose, and UDP but not by other sugar nucleotides, suggesting that RHM2 maintains cytoplasmic levels of UDP-D-glucose and UDP-L-rhamnose via feedback inhibition by UDP-L-rhamnose and UDP-D-xylose.

Reconstruction of de novo pathway for synthesis of UDP-glucuronic acid and UDP-xylose from intrinsic UDP-glucose in Saccharomyces cerevisiae.

Oka T, Jigami Y
FEBS J. 2006; 273: 2645-57

UDP-D-glucuronic acid and UDP-D-xylose are required for the biosynthesis of glycosaminoglycan in mammals and of cell wall polysaccharides in plants. Given the importance of these glycans to some organisms, the development of a system for production of UDP-D-glucuronic acid and UDP-D-xylose from a common precursor could prove useful for a number of applications. The budding yeast Saccharomyces cerevisiae lacks an endogenous ability to synthesize or consume UDP-D-glucuronic acid and UDP-D-xylose. However, yeast have a large cytoplasmic pool of UDP-D-glucose that could be used to synthesize cell wall beta-glucan, as a precursor of UDP-D-glucuronic acid and UDP-D-xylose. Thus, if a mechanism for converting the precursors into the end-products can be identified, yeast may be harnessed as a system for production of glycans. Here we report a novel S. cerevisiae strain that coexpresses the Arabidopsis thaliana genes UGD1 and UXS3, which encode a UDP-glucose dehydrogenase (AtUGD1) and a UDP-glucuronic acid decarboxylase (AtUXS3), respectively, which are required for the conversion of UDP-D-glucose to UDP-D-xylose in plants. The recombinant yeast strain was capable of converting UDP-D-glucose to UDP-D-glucuronic acid, and UDP-D-glucuronic acid to UDP-D-xylose, in the cytoplasm, demonstrating the usefulness of this yeast system for the synthesis of glycans. Furthermore, we observed that overexpression of AtUGD1 caused a reduction in the UDP-D-glucose pool, whereas coexpression of AtUXS3 and AtUGD1 did not result in reduction of the UDP-D-glucose pool. Enzymatic analysis of the purified hexamer His-AtUGD1 revealed that AtUGD1 activity is strongly inhibited by UDP-D-xylose, suggesting that AtUGD1 maintains intracellular levels of UDP-D-glucose in cooperation with AtUXS3 via the inhibition of AtUGD1 by UDP-D-xylose.

Studies on the mechanism of collagen glucosyltransferase reaction.

Myllyla R
Eur J Biochem. 1976; 70: 225-31

The mechanism of collagen glucosyltransferase reaction was studied with enzyme preparations purified about 2500-5000-fold from extract of homogenate of whole chick embryos. Data obtained in experiments on initial velocity and inhibition kinetics of the reaction were consistent with an ordered mechanism in which the substrates are bound to the enzyme in the following order: Mn2+, UDP-glucose and collagen substrate, the addition of Mn2+ being at thermodynamic equilibrium and the binding site of the UDP-glucose to the enzyme not being the same as that for Mn2+ and collagen substrate. Only one metal co-factor seems to be involved in the reaction. The collagen substrate can probably also react in some conditions with enzyme-Mn2+ and with enzyme-Mn2+-UDP, and the UDP with the free enzyme, but in all these instances dead-end complexes are formed. Evidence is presented for an ordered release of the products in the following order: glucosylated collagen, UDP and Mn2+, in which Mn2+ need not leave the enzyme during each catalytic cycle.

First molecular characterization of a uridine diphosphate galacturonate 4-epimerase: an enzyme required for capsular biosynthesis in Streptococcus pneumoniae type 1.

Munoz R, Lopez R, de Frutos M, Garcia E
Mol Microbiol. 1999; 31: 703-13

Uridine diphosphate galacturonate 4-epimerases (UDPGLEs) are enzymes that convert UDP-glucuronate into UDP-galacturonate. Although the presence of UDPGLEs has been reported in prokaryoic and eukaryotic organisms, the genes coding for these enzymes are completely unknown. The galacturonic acid-containing capsular polysaccharide of Streptococcus pneumoniae type 1 is synthesized through the action of a specific UDPGLE. We have constructed a defined deletion mutant in the cap1J gene (one of the 15 cap1 genes responsible for the synthesis of the type 1 capsule) that exhibited an unencapsulated phenotype. This mutant was unable to synthesize UDPGLE, suggesting that Cap1J was the type 1-specific UDPGLE of S. pneumoniae. Escherichia coli cells harbouring the recombinant plasmid pRMM38 (cap1J) overproduced a 40 kDa protein, characterized as Cap1J on the basis of the N-terminal amino acid sequence analysis, and expressed high levels of enzymatically active Cap1J epimerase. Cap1J was partially purified, although purification to electrophoretic homogeneity inactivated the enzyme irreversibly. The enzyme has the following characteristics: K(m) for UDP-glucuronate, 0.24 mM; pH optimum, 7.5; equilibrium constant (in the direction of UDP-galacturonate formation), 1.3; and an approximate M(r) of 80,000 for the active form. The Cap1J protein exhibited a fluorescence emission spectrum similar to that of NADH. Upon inactivation with p-hydroxymercuribenzoate, the addition of NAD+ and 2-mercaptoethanol were sufficient to reactivate the enzyme. Among several compounds tested, UDP-galactose and UDP-xylose exhibited the highest inhibition of the UDPGLE activity. Inactivation of UDPGLE activity was also observed in the presence of UMP and several reducing sugars. To our knowledge, this is the first example of a thoroughly molecular characterization of a UDPGLE.

Resolution, purification and some properties of the multiple forms of cellobiose quinone dehydrogenase from the white-rot fungus Sporotrichum pulverulentum.

Morpeth FF, Jones GD
Biochem J. 1986; 236: 221-6

Four forms of cellobiose quinone dehydrogenase have been purified from the white-rot fungus Sporotrichum pulverulentum. The Mr of the enzyme has been estimated by sedimentation equilibrium to be 57,800 and by SDS/polyacrylamide-gel to be 60,000. These enzymes are clearly monomers. Cellobiose quinone dehydrogenases contain FAD and variable amounts of a green chromophore which we suggest is 6-hydroxy-FAD. The superoxide anion and H2O2 are the products of its reaction with oxygen. All of the isoenzymes from any one preparation display similar kinetic parameters. However, these vary between preparations. The only apparent difference between the four separable isoenzymes is their neutral-sugar content.

Xylosyl transfer to an endogenous renal acceptor. Characteristics of the reaction and properties of the product.

Meezan E, Ananth S, Manzella S, Campbell P, Siegal S, Pillion DJ, Roden L
J Biol Chem. 1994; 269: 11503-8

In the course of a study of UDP-xylose:proteoglycan core protein xylosyltransferase (EC 2.4.2.26), another xylosyltransferase was discovered in the soluble fraction of a rat kidney homogenate. The latter enzyme catalyzed [3H]xylosyl transfer from UDP-[3H]xylose to an endogenous acceptor and yielded a product in which the xylose was bound by an alkali-stable linkage. It was therefore concluded that the acceptor was not the core protein of one of the proteoglycans containing a xylose-->serine linkage, since this linkage is cleaved by alkali. The [3H]xylose-labeled product emerged with the void volume when chromatographed on Sephadex G-50, it was precipitated by trichloroacetic acid, and it had a mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis corresponding to a molecular mass of about 32,000 Da. Digestion with trypsin or alpha-amylase degraded the labeled product to small fragments, as determined by gel chromatography, suggesting that it was a glycoprotein related to glycogen. A product of similar characteristics was formed when UDP-[3H]glucose was substituted for UDP-[3H]xylose as the glycosyl donor, and the two nucleotide sugars were mutually competitive in the respective transfer reactions, indicating that they were substrates for the same enzyme. On the basis of these findings, it was tentatively concluded that the xylosyltransferase and its acceptor were the renal form of glycogenin.

Mechanistic roles of tyrosine 149 and serine 124 in UDP-galactose 4-epimerase from Escherichia coli.

Liu Y, Thoden JB, Kim J, Berger E, Gulick AM, Ruzicka FJ, Holden HM, Frey PA
Biochemistry. 1997; 36: 10675-84

Synthesis and overexpression of a gene encoding Escherichia coli UDP-galactose 4-epimerase and engineered to facilitate cassette mutagenesis are described. General acid-base catalysis at the active site of this epimerase has been studied by kinetic and spectroscopic analysis of the wild-type enzyme and its specifically mutated forms Y149F, S124A, S124V, and S124T. The X-ray crystal structure of Y149F as its abortive complex with UDP-glucose is structurally similar to that of the corresponding wild-type complex, except for the absence of the phenolic oxygen of Tyr 149. The major effects of mutations are expressed in the values of kcat and kcat/Km. The least active mutant is Y149F, for which the value of kcat is 0.010% of that of the wild-type epimerase. The activity of S124A is also very low, with a kcat value that is 0.035% of that of the native enzyme. The values of Km for Y149F and S124A are 12 and 21% of that of the wild-type enzyme, respectively. The value of kcat for S124T is about 30% of that of the wild-type enzyme, and the value of Km is similar to that of the native enzyme. The reactivities of the mutants in UMP-dependent reductive inactivation by glucose are similarly affected, with kobs being decreased by 6560-, 370-, and 3.4-fold for Y149F, S124A, and S124T, respectively. The second-order rate constants for reductive inactivation by NaBH3CN, which does not require general base catalysis, are similar to that for the native enzyme in the cases of S124A, S124T, and S124V. However, Y149F reacts with NaBH3CN 12-20-fold faster than the wild-type enzyme at pH 8.5 and 7.0, respectively. The increased rate for Y149F is attributed to the weakened charge-transfer interaction between Phe 149 and NAD+, which is present with Tyr 149 in the wild-type enzyme. The charge-transfer band is present in the serine mutants, and its intensity at 320 nm is pH-dependent. The pH dependencies of A320 showed that the pKa values for Tyr 149 are 6.08 for the wild-type epimerase, 6.71 for S124A, 6.86 for S124V, and 6.28 for S124T. The low pKa value for Tyr 149 is attributed mainly to the positive electrostatic field created by NAD+ and Lys 153 (4.5 kcal mol-1) and partly to hydrogen bonding with Ser 124 (1 kcal mol-1). The pKa of Tyr 149 is the same as the kinetic pKa for the Bronsted base that facilitates hydride transfer to NAD+. We concluded that Tyr 149 provides the driving force for general acid-base catalysis, with Ser 124 playing an important role in mediating proton transfer.

Microbial biosynthesis of the anticoagulant precursor 4-hydroxycoumarin.

Lin Y, Shen X, Yuan Q, Yan Y
Nat Commun. 2013; 4: 2603-2603

4-Hydroxycoumarin (4HC) type anticoagulants (for example, warfarin) are known to have a significant role in the treatment of thromboembolic diseases--a leading cause of patient morbidity and mortality worldwide. 4HC serves as an immediate precursor of these synthetic anticoagulants. Although 4HC was initially identified as a naturally occurring product, its biosynthesis has not been fully elucidated. Here we present the design, validation, in vitro diagnosis and optimization of an artificial biosynthetic mechanism leading to the microbial biosynthesis of 4HC. Remarkably, function-based enzyme bioprospecting leads to the identification of a characteristic FabH-like quinolone synthase from Pseudomonas aeruginosa with high efficiency on the 4HC-forming reaction, which promotes the high-level de novo biosynthesis of 4HC in Escherichia coli (~500 mg l(-)(1) in shake flasks) and further in situ semisynthesis of warfarin. This work has the potential to be scaled-up for microbial production of 4HC and opens up the possibility of biosynthesizing diverse coumarin molecules with pharmaceutical importance.

Effects of ambroxol on alginate of mature Pseudomonas aeruginosa biofilms.

Li F, Yu J, Yang H, Wan Z, Bai D
Curr Microbiol. 2008; 57: 1-7

Biofilm-forming bacteria Pseudomonas aeruginosa is a common pathogen in mechanically ventilated newborns, which can cause life-threatening infections. Alginate of mucoid Pseudomonas aeruginosa biofilms is considered an important virulence factor which contributes to the resistance to antibiotics. Traditionally, ambroxol is widely used in newborns with lung problems as a mucolytic agent and antioxidant agent as well. And there are few studies that demonstrated the anti-biofilm activity of ambroxol. In this study, we found that ambroxol can affect the structure of mucoid Pseudomonas aeruginosa biofilms. Further, we found that ambroxol reduces the production of alginate, the expression of the important genes and the activity of key enzyme guanosine diphospho-D-mannose dehydrogenase (GDP-mannose dehydrogenase; GMD) which were involved in alginate biosynthesis.

Control of uridine diphosphate-glucose dehydrogenase synthesis and uridine diphosphate-glucuronic acid accumulation by a regulator gene mutation in Escherichia coli K-12.

Lieberman MM, Shaparis A, Markovitz A
J Bacteriol. 1970; 101: 959-64

Uridine diphosphate (UDP)-glucose dehydrogenase, the enzyme that converts UDP-glucose to UDP-glucuronic acid, was derepressed in a mucoid (capR9) strain of Escherichia coli K-12 and repressed in a nonmucoid (capR(+)) strain. A nonmucoid mutant (strain MC 152; capR9 non-2) derived from the mucoid strain accumulated large quantities of nucleotides. Among these nucleotides, UDP-glucuronic acid was identified as well as guanosine triphosphate and an adenosine diphosphate-sugar. UDP-glucose dehydrogenase was still derepressed in strain MC 152. When the nonmucoid mutant was transduced to the wild-type state for this regulator gene (capR(+)), the transductant was found to accumulate less total nucleotides, and the accumulation of UDP-glucuronic acid was abolished. UDP-glucose dehydrogenase was repressed in the capR(+)non-2 strain but not to the same extent that it was in the capR(+) strain.

Inhibition of uridine diphosphate glucose dehydrogenase by a free radical formed from chlorpromazine.

Levy L, Burbridge TN
Biochem Pharmacol. 1967; 16: 1249-60

Oxygen-dependent alginate synthesis and enzymes in Pseudomonas aeruginosa.

Leitao JH, Sa-Correia I
J Gen Microbiol. 1993; 139: 441-5

Alginate production by the highly alginate-producing Pseudomonas aeruginosa 8821M was maximal at a dissolved oxygen tension (DOT) of 5% of air saturation. Lower DOT limited growth and alginate synthesis. At higher DOT values up to 70% of air saturation, the specific alginate production rate decreased. Nevertheless, the molecular mass of the alginate increased at higher aerations, as indicated by the viscosity of solutions of the isolated biopolymer. The specific activity of the four enzymes leading to GDP-mannuronic acid formation, phosphomannose isomerase (PMI), phosphomannomutase (PMM), GDP-mannose pyrophosphorylase (GMP) and GDP-mannose dehydrogenase (GMD), increased with DOT of up to 25%. At higher DOT, however, only GMP and GMD maintained their maximum values. Changes observed at high oxygen concentrations in the relative activities of PMI and GMP, which are activities of the same bifunctional protein, were attributed to the much higher sensitivity of PMI activity to irreversible oxidative inactivation. The less pronounced decrease of PMM activity at high DOT correlated with an intermediate sensitivity to oxidative inactivation, but could also be related to sequential induction of PMM by the product of the PMI reaction. Thus, oxygen-dependence of alginate synthesis was at least partially the effect of DOT on GDP-mannuronic acid formation. Optimal aerations for maximal alginate production (DOT = 5-10%) were below the aeration level (70%) that led to the highest viscosity. These results suggest that, like GMD, polymerization activity is not very sensitive to oxidative inactivation and they are consistent with the hypothesis that polymerization is dependent on GMD activity, or is regulated in a similar way.

Effects of growth temperature on alginate synthesis and enzymes in Pseudomonas aeruginosa variants.

Leitao JH, Fialho AM, Sa-Correia I
J Gen Microbiol. 1992; 138: 605-10

Spontaneous variation of the level of alginate synthesis in Pseudomonas aeruginosa was associated with changes in the activity of all four enzymes leading to synthesis of GDP-mannuronic acid, the activated precursor for polymerization. For the high-alginate-producing variant 8821M, alginate yield and properties, as well as the levels of alginate enzymes, were dependent on growth temperature. In contrast, levels of alginate and enzymes in the mucoid parent strain 8821 were very low and near temperature-independent. The difference in the specific activity of GDP-mannose dehydrogenase (GMD), encoded by the algD gene, between the two strains was associated with the alginate biosynthetic ability and with the degree of activation of the algD promoter, measured using the algD-xylE transcription fusion on plasmid pVD2X. Maximal activity of the four enzymes was observed in strain 8821M grown at 30 degrees C, a temperature below the optimum for growth (35 degrees C). The effect of temperature on GMD activity could not be explained by the regulation of the algD promoter by temperature, since expression of pVDZX appeared to be more active at 35 degrees C, when the decrease of pVD2X copy number with increasing temperature was taken into account. The involvement of enzymes that catalyse steps downstream from the formation of the activated precursor should also be considered, as suggested by differences in the molecular mass of alginates synthesized by the two strains at various temperatures. Acetyl content of alginates increased as temperature decreased and strain 8821M produced the highest levels of acetylated polymers. The degree of acetylation appeared to be related to growth rate and could reflect acetyl-CoA availability.

Identification of amino acid residues important for the phosphomannose isomerase activity of PslB in Pseudomonas aeruginosa PAO1.

Lee HJ, Chang HY, Venkatesan N, Peng HL
FEBS Lett. 2008; 582: 3479-83

Phosphomannose isomerase (PMI) plays a pivotal role in biosynthesis of GDP-mannose, an important precursor of many polysaccharides. We demonstrate in this study that Pseudomonas aeruginosa pslB encodes a protein with GDP-mannose pyrophosphorylase/PMI dual activities. The PMI activity is Co2+-dependent and could be inhibited by GDP-mannose in a competitive manner. Furthermore, the activity could be inactivated by 2,3-butanedione suggesting the presence of a catalytic Arg residue. Site-specific mutations at R373, R472, R479, E410, H411, N433 and E458 increase the KM approximately 8-20-fold. The PMI activity of PslB was completely diminished with a R408K or R408A, reflecting the importance of this residue in catalysis. Overall, these results provide a basis for understanding the catalytic mechanism of PMI.

Steady-state kinetics of cabbage histidinol dehydrogenase.

Kheirolomoom A, Mano J, Nagai A, Ogawa A, Iwasaki G, Ohta D
Arch Biochem Biophys. 1994; 312: 493-500

Cabbage histidinol dehydrogenase (HDH) oxidizes L-histidinol to L-histidine through two sequential NAD(+)-linked reactions via an alkaline-labile, L-histidinaldehyde intermediate. The kinetic mechanism of the overall reaction as well as the partial reactions involved in the overall catalysis were investigated at pH 7.2 using L-histidinaldehyde as a substrate. Product inhibition patterns conformed to a Bi Uni Uni Bi Ping Pong mechanism as reported for the HDH from Salmonella typhimurium. Thus, the reaction scheme is ordered with the binding of histidinol first and NAD+ second, and histidine is the last product to be released. The intermediate, L-histidinaldehyde, could be a substrate for both the oxidation and the reduction reactions to produce histidine and histidinol, respectively. L-Histidine was not enzymatically reduced in the presence of NADH, indicating that the reaction to oxidize histidinaldehyde is apparently irreversible. L-Histidinaldehyde exhibited a three times greater binding rate constant than histidinol with a considerably small dissociation constant. These results were in agreement with the observation that histidinaldehyde was not released during the overall reaction. The rate of the reduction of histidinaldehyde to histidinol was almost same as that of the overall oxidation reaction. The overall oxidation from histidinol to histidine proceeded about three times slower than the partial oxidation from histidinaldehyde to histidine, suggesting that the first-half forward reaction is the rate-determining step in the total reaction of cabbage HDH.

Biosynthesis of UDP-N-acetyl-D-glucosaminuronic acid and UDP-N-acetyl-D-mannosaminuronic acid in Micrococcus luteus.

Kawamura T, Ichihara N, Sugiyama S, Yokota H, Ishimoto N, Ito E
J Biochem. 1985; 98: 105-16

The occurrence and formation of UDP-N-acetyl-D-glucosaminuronic acid (UDP-GlcNAcA) and UDP-N-acetyl-D-mannosaminuronic acid (UDP-ManNAcA) were studied in Micrococcus luteus ATCC 4698. UDP-N-acetylhexosaminuronic acid separated from D-cycloserine-inhibited cells was shown to be a mixture of UDP-GlcNAcA and UDP-ManNAcA in the ratio of 87:13, whereas that obtained from untreated cells was a 96:4 mixture of these two nucleotides. Crude enzyme preparations obtained from the supernatant fraction of cells catalyzed the NAD+-dependent conversion of UDP-GlcNAc into UDP-GlcNAcA and UDP-ManNAcA. Studies on the partial separation and properties of enzymes revealed that UDP-GlcNAcA is synthesized directly from UDP-GlcNAc by the action of UDP-GlcNAc dehydrogenase and that UDP-ManNAcA is synthesized from UDP-GlcNAc through the successive actions of UDP-GlcNAc 2-epimerase and UDP-ManNAc dehydrogenase. However, enzymatic conversion of UDP-GlcNAcA to UDP-ManNAcA was not detected. Ammonium sulfate protects both dehydrogenases from inactivation during storage and incubation. Partially purified UDP-GlcNAc dehydrogenase required dithiothreitol and the particulate fraction for its full activity. The apparent Km values of UDP-GlcNAc dehydrogenase for UDP-GlcNAc and NAD+ were 0.28 and 1.43 mM, respectively. The optimum pH of this enzyme was higher than 9 in Tris-HCl buffer. p-Chloromercuribenzoate at 27 microM as well as 10 mM ethanol almost completely inhibited the UDP-GlcNAc dehydrogenase reaction.

Succinyl coenzyme A synthetase of Pseudomonas aeruginosa with a broad specificity for nucleoside triphosphate (NTP) synthesis modulates specificity for NTP synthesis by the 12-kilodalton form of nucleoside diphosphate kinase.

Kapatral V, Bina X, Chakrabarty AM
J Bacteriol. 2000; 182: 1333-9

Pseudomonas aeruginosa secretes copious amounts of an exopolysaccharide called alginate during infection in the lungs of cystic fibrosis patients. A mutation in the algR2 gene of mucoid P. aeruginosa is known to exhibit a nonmucoid (nonalginate-producing) phenotype and showed reduced activities of succinyl-coenzyme A (CoA) synthetase (Scs) and nucleoside diphosphate kinase (Ndk), implying coregulation of Ndk and Scs in alginate synthesis. We have cloned and characterized the sucCD operon encoding the alpha and beta subunits of Scs from P. aeruginosa and have studied the role of Scs in generating GTP, an important precursor in alginate synthesis. We demonstrate that, in the presence of GDP, Scs synthesizes GTP using ATP as the phosphodonor and, in the presence of ADP, Scs synthesizes ATP using GTP as a phosphodonor. In the presence of inorganic orthophosphate, succinyl-CoA, and an equimolar amount of ADP and GDP, Scs synthesizes essentially an equimolar amount of ATP and GTP. Such a mechanism of GTP synthesis can be an alternate source for the synthesis of alginate as well as for the synthesis of other macromolecules requiring GTP such as RNA and protein. Scs from P. aeruginosa is also shown to exhibit a broad NDP kinase activity. In the presence of inorganic orthophosphate (P(i)), succinyl-CoA, and either GDP, ADP, UDP or CDP, it synthesizes GTP, ATP, UTP, or CTP. Scs was previously shown to copurify with Ndk, presumably as a complex. In mucoid cells of P. aeruginosa, Ndk is also known to exist in two forms, a 16-kDa cytoplasmic form predominant in the log phase and a 12-kDa membrane-associated form predominant in the stationary phase. We have observed that the 16-kDa Ndk-Scs complex present in nonmucoid cells, synthesizes all three of the nucleoside triphosphates from a mixture of GDP, UDP, and CDP, whereas the 12-kDa Ndk-Scs complex specifically present in mucoid cell predominantly synthesizes GTP and UTP but not CTP. Such regulation may promote GTP synthesis in the stationary phase when the bulk of alginate is synthesized by mucoid P. aeruginosa.

Hysteresis and negative cooperativity in human UDP-glucose dehydrogenase.

Kadirvelraj R, Sennett NC, Custer GS, Phillips RS, Wood ZA
Biochemistry. 2013; 52: 1456-65

Human UDP-alpha-d-glucose 6-dehydrogenase (hUGDH) forms a hexamer that catalyzes the NAD(+)-dependent oxidation of UDP-alpha-d-glucose (UDG) to produce UDP-alpha-d-glucuronic acid. Mammalian UGDH displays hysteresis (observed as a lag in progress curves), indicating that the enzyme undergoes a slow transition from an inactive to an active state. Here we show that hUGDH is sensitive to product inhibition during the lag. The inhibition results in a systematic decrease in steady-state velocity and makes the lag appear to have a second-order dependence on enzyme concentration. Using transient-state kinetics, we confirm that the lag is in fact due to a substrate and cofactor-induced isomerization of the enzyme. We also show that the cofactor binds to the hUGDH:UDG complex with negative cooperativity. This suggests that the isomerization may be related to the formation of an asymmetric enzyme complex. We propose that the hysteresis in hUGDH is the consequence of a functional adaptation; by slowing the response of hUGDH to sudden increases in the flux of UDG, the other biochemical pathways that use this important metabolite (i.e., glycolysis) will have a competitive edge.

Purification, biochemical and molecular characterization of a metalloprotease from Pseudomonas aeruginosa MN7 grown on shrimp wastes.

Jellouli K, Bayoudh A, Manni L, Agrebi R, Nasri M
Appl Microbiol Biotechnol. 2008; 79: 989-99

A protease-producing bacterium was isolated and identified as Pseudomonas aeruginosa MN7. The strain was found to produce proteases when it was grown in media containing only shrimp waste powder (SWP), indicating that it can obtain its carbon, nitrogen, and salts requirements directly from shrimp waste. The use of 60 g/l SWP resulted in a high protease production. Elastase, the major protease produced by P. aeruginosa MN7, was purified from the culture supernatant to homogeneity using acetone precipitation, Sephadex G-75 gel filtration, and ultrafiltration using a 10-kDa cut-off membrane, with a 5.2-fold increase in specific activity and 38.4% recovery. The molecular weight of the purified elastase was estimated to be 34 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration. The optimum temperature and pH for protease activity were 60 degrees C and 8.0, respectively. The activity of the enzyme was totally lost in the presence of ethylene glycol tetraacetic acid, suggesting that the purified enzyme is a metalloprotease. The purified enzyme was highly stable in the presence of organic solvents, retaining 100% of its initial activity after 60 days of incubation at 30 degrees C in the presence of dimethyl sulfoxide and methanol. The lasB gene, encoding the MN7 elastase, was isolated and its DNA sequence was determined.

Purification and characterization of D-glucosaminitol dehydrogenase from Agrobacterium radiobacter.

Iwamoto R, Sakamoto C, Tamura K, Mikata Y, Tanaka M
Biosci Biotechnol Biochem. 1999; 63: 785-91

D-Glucosaminitol dehydrogenase, which catalyzes the conversion of D-glucosaminitol to 3-keto-D-glucosaminitol, was purified to apparent homogeneity from extracts of Agrobacterium radiobacter. This organism has constitutively depressed levels of the enzyme but expression of the enzyme is induced by addition of D-glucosamine to the medium. Purification included ammonium sulfate fractionation and chromatography on columns of DEAE-Sephacel, Octyl-Sepharose CL-4B, and Cellulofine. The purified enzyme migrated as a single band, coinciding with dehydrogenase activities specific for D-glucosaminitol and ethanol, when electrophoresed on a 7.5% polyacrylamide gel at pH 8.0. Electrophoresis on a 12.5% PAGE in the presence of 1% SDS also yielded a single band. The enzyme had an apparent molecular mass of 79 kDa, as measured by the pattern of elution from a column of Cellulofine. The results indicated that the enzyme was a dimer of identical (or nearly identical) subunits of 39.5 kDa. D-Glucosaminitol dehydrogenase required NAD+ as a cofactor and used ethanol as the preferred substrate, as well as aliphatic alcohols with 2 to 4 carbon atoms, D-glucosaminitol, D-glucosaminate, DL-allothreonine, glycerol, and erythritol as additional substrates. In 50 mM Tris-HCl buffer (pH 9.0) at 25 degrees C, the K(m) for D-glucosaminitol, ethanol, and NAD+ were 2.2, 2.0, and 0.08 mM, respectively. The enzyme had a pH optimum of 10 for D-glucosaminitol and 8.5 for ethanol. The enzyme lost substantial activity when treated with pyrazole, with certain reagents that react with sulfhydryl groups and with Zn2+ ion. The various results together suggest that the enzyme exploits different amino acid residues for the dehydrogenation of ethanol and of D-glucosaminitol.

Characterization of salt-regulated mannitol-1-phosphate dehydrogenase in the red alga Caloglossa continua.

Iwamoto K, Kawanobe H, Ikawa T, Shiraiwa Y
Plant Physiol. 2003; 133: 893-900

Mannitol-1-phosphate (M1P) dehydrogenase (M1PDH; EC 1.1.1.17), an enzyme catalyzing the reduction of Fru-6-phosphate (F6P) to M1P in algal mannitol biosynthesis, was purified to homogeneity from a cell homogenate of the eulittoral red alga Caloglossa continua (Okamura) King et Puttock. The enzyme was a monomer with an apparent molecular mass of 53 kD, as determined by gel filtration and SDS-PAGE, and exhibited an pI of approximately 5.5. The substrate specificity was very high toward F6P and M1P for respective reductive and oxidative reactions. The enzyme was found to be a sulfhydryl-type, because its activity was inhibited by N-ethylmaleimide and p-hydroxymercuribenzoate, and the inhibition by p-hydroxymercuribenzoate was rescued by 2-mercaptoethanol. Some unknown factors in the extract may also have inhibited the activity, because the total activity was greatly increased through the purification procedure. The optimum pH for F6P reduction was changed from 6.0 or lower to 7.2 by the addition of 200 mm NaCl. The reduction of F6P showed strong substrate inhibition above 0.5 mm. However, Km(F6P) of M1PDH was increased eight times by the addition of 200 mm NaCl, whereas Vmax was in a similar range with the avoidance of substrate inhibition by F6P. These results indicate that the enzyme was finely and directly regulated by the salt concentration without the requirement for gene expression. M1PDH can therefore be a key enzyme for regulating mannitol biosynthesis when the alga is stressed by a salinity change.

UDP-glucose dehydrogenase polymorphisms from patients with congenital heart valve defects disrupt enzyme stability and quaternary assembly.

Hyde AS, Farmer EL, Easley KE, van Lammeren K, Christoffels VM, Barycki JJ, Bakkers J, Simpson MA
J Biol Chem. 2012; 287: 32708-16

Cardiac valve defects are a common congenital heart malformation and a significant clinical problem. Defining molecular factors in cardiac valve development has facilitated identification of underlying causes of valve malformation. Gene disruption in zebrafish revealed a critical role for UDP-glucose dehydrogenase (UGDH) in valve development, so this gene was screened for polymorphisms in a patient population suffering from cardiac valve defects. Two genetic substitutions were identified and predicted to encode missense mutations of arginine 141 to cysteine and glutamate 416 to aspartate, respectively. Using a zebrafish model of defective heart valve formation caused by morpholino oligonucleotide knockdown of UGDH, transcripts encoding the UGDH R141C or E416D mutant enzymes were unable to restore cardiac valve formation and could only partially rescue cardiac edema. Characterization of the mutant recombinant enzymes purified from Escherichia coli revealed modest alterations in the enzymatic activity of the mutants and a significant reduction in the half-life of enzyme activity at 37 degrees C. This reduction in activity could be propagated to the wild-type enzyme in a 1:1 mixed reaction. Furthermore, the quaternary structure of both mutants, normally hexameric, was destabilized to favor the dimeric species, and the intrinsic thermal stability of the R141C mutant was highly compromised. The results are consistent with the reduced function of both missense mutations significantly reducing the ability of UGDH to provide precursors for cardiac cushion formation, which is essential to subsequent valve formation. The identification of these polymorphisms in patient populations will help identify families genetically at risk for valve defects.

Identification of a UDP-glucose-binding site of human UDP-glucose dehydrogenase by photoaffinity labeling and cassette mutagenesis.

Huh JW, Lee HJ, Choi MM, Yang SJ, Yoon SY, Kim DW, Kim SY, Choi SY, Cho SW
Bioconjug Chem. 2005; 16: 710-6

We have identified a UDP-glucose-binding site within human UDP-glucose dehydrogenase (hUGDH) by photoaffinity labeling with a specific probe, [(32)P]5N(3)UDP-glucose, and cassette mutagenesis using a synthetic hUGDH gene. Photolabel-containing peptides were generated by photolysis followed by tryptic digestion and isolated using the phosphopeptide isolation kit. Photolabeling of these peptides was effectively prevented by the presence of UDP-glucose during photolysis, demonstrating a selectivity of the photoprobe for the UDP-glucose-binding site. Amino acid sequencing and compositional analysis identified the UDP-glucose-binding site of hUGDH as the region containing the sequence, ASVGFGGSXFQK, corresponding to A268-K279 of the amino acid sequence of hUGDH. The unidentified residue, X, can be designated as a photolabeled C276 because the sequences including the cysteine residue in question have a complete identity with those of other UGDH species known. The importance of the C276 residue in the binding of UDP-glucose was further examined with mutant proteins at the C276 site. The mutagenesis at C276 has no effect on the expression of the mutants (C276G, C276K, C276E, C276L, and C276Y). Enzyme activities of the C276 mutants were not measurable under normal assay conditions, suggesting an important role for the C276 residue. No incorporation of [(32)P]5N(3)UDP-glucose was also observed for the mutants. These results indicate that C276 plays an important role for efficient binding of UDP-glucose to hUGDH.

Hepatic UDP-glucuronic acid regulation during acetaminophen biotransformation in rats.

Hjelle JJ
J Pharmacol Exp Ther. 1986; 237: 750-6

Acetaminophen (AA) glucuronidation is capacity limited in several species after administration of high doses and previous data indicate that this phenomenon is due probably to a decrease in the concentration of the reaction cosubstrate UDP-glucuronic acid in liver. The rate-limiting determinant in UDP-glucuronic acid synthesis during AA glucuronidation is not known. The objective of the present study was to determine whether UDP-glucuronic acid synthesis during AA biotransformation is restricted by the supply of UDP-glucose or is limited by UDP-glucose dehydrogenase activity. Adult male Sprague-Dawley rats were injected with 600 mg/kg i.p of AA and liver was obtained 30, 60, 120 and 240 min later for quantitation of UDP-glucose, glycogen and UDP-glucuronic acid. AA was found to decrease markedly UDP-glucuronic acid concentration in liver 30, 60 and 120 min after injection (28, 52 and 58% of control values, respectively). In contrast, hepatic UDP-glucose levels were not altered after 30 min, but were decreased to 55 and 68% of control values 60 and 120 min after AA administration. Glycogen concentrations were decreased at the 30-min time interval only (78% of control). Therefore, maximal depletion of UDP-glucuronic acid occurred when UDP-glucose levels were not affected. UDP-glucose dehydrogenase is subject to product inhibition by NADH and UDP-glucuronic acid and it is possible that NADH accumulates during rapid utilization of UDP-glucuronic acid. Consequently, the effects of AA on cytosolic NADH/NAD ratios in liver were examined by determining the lactate/pyruvate ratio.(ABSTRACT TRUNCATED AT 250 WORDS)

Cloning and characterization of the Pseudomonas aeruginosa sodA and sodB genes encoding manganese- and iron-cofactored superoxide dismutase: demonstration of increased manganese superoxide dismutase activity in alginate-producing bacteria.

Hassett DJ, Woodruff WA, Wozniak DJ, Vasil ML, Cohen MS, Ohman DE
J Bacteriol. 1993; 175: 7658-65

Pseudomonas aeruginosa is a strict aerobe which is likely exposed to oxygen reduction products including superoxide and hydrogen peroxide during the metabolism of molecular oxygen. To counterbalance the potentially hazardous effects of elevated endogenous levels of superoxide, most aerobic organisms possess one or more superoxide dismutases or compounds capable of scavenging superoxide. We have previously shown that P. aeruginosa possesses both an iron- and a manganese-cofactored superoxide dismutase (D. J. Hassett, L. Charniga, K. A. Bean, D. E. Ohman, and M. S. Cohen, Infect. Immun. 60:328-336, 1992). In this study, the genes encoding manganese (sodA)- and iron (sodB)- cofactored superoxide dismutase were cloned by using a cosmid library of P. aeruginosa FRD which complemented an Escherichia coli (JI132) strain devoid of superoxide dismutase activity. The sodA and sodB genes of P. aeruginosa, when cloned into a high-copy-number vector (pKS-), partially restored the aerobic growth rate defect, characteristic of the Sod- strain, to that of the wild type (AB1157) when grown in Luria broth. The nucleotide sequences of sodA and sodB have open reading frames of 612 and 579 bp that encode dimeric proteins of 22.9 and 21.2 kDa, respectively. These data were also supported by the results of in vitro expression studies. The deduced amino acid sequence of the P. aeruginosa manganese and iron superoxide dismutase revealed approximately 50 and 67% similarity with manganese and iron superoxide dismutases from E. coli, respectively. There was also remarkable similarity with iron and manganese superoxide dismutases from other phyla. The mRNA start site of sodB was mapped to 174 bp upstream of the ATG codon. A likely promoter with similarity to the -10 and -35 consensus sequence of E. coli was observed upstream of the ATG start codon of sodB. Regions sequenced 519 bp upstream of the sodA electrophoresis, sodA gene revealed no such promoter, suggesting an alternative mode of control for sodA. By transverse field electrophoresis, sodA and sodB were mapped to the 71- to 75-min region on the P. aeruginosa PAO1 chromosome. Strikingly, mucoid alginate-producing bacteria generated greater levels of manganese superoxide dismutase than nonmucoid revertants, suggesting that mucoid P. aeruginosa is responding to oxidative stress and/or changes in the redox status of the cell.

Alginase enzyme production by Bacillus circulans.

Hansen JB, Doubet RS, Ram J
Appl Environ Microbiol. 1984; 47: 704-9

Stream and soil samples were screened for microorganisms that would use alginate from mucoid Pseudomonas aeruginosa as the sole carbon and energy source. A pure culture containing large aerobic rods was isolated. The cells were about 0.8 by 2.5 microns in size, had lateral or peritrichous flagella, had a negative Gram stain reaction, and produced spores on sporulation medium. Purified DNA was approximately 46 mol% G+C as measured by thermal denaturation. From these and other biochemical tests, the organism was identified as Bacillus circulans. The enzyme activity that degraded alginate appeared in the culture medium. Upon gel filtration, alginase activity eluted as a single peak at a position corresponding to a protein of 40,000 daltons. Activity recovered from this one-step, partial purification showed apparent endomannuronidase specificity. Like other alginases previously reported, the enzyme appeared likely to be a lyase (or eliminase). However, no Bacillus species or other gram-positive bacteria have heretofore been reported to produce extracellular enzymes with alginase activity. Several other B. circulans strains from the American Type Culture Collection also appeared to have inducible extracellular alginase activity.

UDP-glucose dehydrogenase plays multiple roles in the biology of the pathogenic fungus Cryptococcus neoformans.

Griffith CL, Klutts JS, Zhang L, Levery SB, Doering TL
J Biol Chem. 2004; 279: 51669-76

Cryptococcus neoformans is a pathogenic fungus surrounded by an elaborate polysaccharide capsule that is strictly required for its virulence in humans and other mammals. Nearly half of the sugar residues in the capsule are derived from UDP-glucuronic acid or its metabolites. To examine the role of these nucleotide sugars in C. neoformans, the gene encoding UDP-glucose dehydrogenase was disrupted. Mass spectrometry analysis of nucleotide sugar pools showed that the resulting mutant lacked both UDP-glucuronic acid and its downstream product, UDP-xylose, thus confirming the effect of the knockout and indicating that an alternate pathway for UDP-glucuronic acid production was not used. The mutant was dramatically affected by the lack of specific sugar donors, demonstrating altered cell integrity, temperature sensitivity, lack of growth in an animal model of cryptococcosis, and morphological defects. Additionally, the polysaccharide capsule could not be detected on the mutant cells, although the possibility remains that abbreviated forms of capsule components are made, possibly without proper surface display. The capsule defect is largely independent of the other observed changes, as cells that are acapsular because of mutations in other genes show lack of virulence but do not exhibit alterations in cell integrity, temperature sensitivity, or cellular morphology. All of the observed alterations were reversed by correction of the gene disruption.

Purification and properties of extracellular lipase from Pseudomonas aeruginosa EF2.

Gilbert EJ, Cornish A, Jones CW
J Gen Microbiol. 1991; 137: 2223-9

Extracellular lipase was purified from a Tween 80-limited continuous culture of Pseudomonas aeruginosa EF2 by ultrafiltration of the culture supernatant followed by anion-exchange and gel-filtration FPLC. The lipase was composed of a single subunit (Mr 29,000, pI 4.9), which was capable of a variable degree of aggregation, and which exhibited both lipase activity, measured with the insoluble substrate olive oil (predominantly triolein), and esterase activity, measured with the soluble substrates p-nitrophenyl acetate and Tween 80. Lipase activity was approximately eight times higher than either type of esterase activity (kcat approximately 3000 s-1 for the hydrolysis of olive oil). The enzyme showed a marked regiospecificity for the 1,3-oleyl residues of radiolabelled triolein, was relatively stable at moderate temperatures (exhibiting a biphasic loss of activity with an initial t1/2 of 17.5 min at 60 degrees C) and was very stable to freezing and thawing. Lipase activity was only weakly inhibited by the serine-active reagent 3,4-dichloroisocoumarin, and was not inhibited by the chelating agent EDTA (1 mM). The N-terminal amino acid sequence of the Ps. aeruginosa EF2 lipase showed a marked similarity to those of several other bacterial lipases.

Determination of 4-hydroxyproline-2-epimerase activity by capillary electrophoresis: A stereoselective platform for inhibitor screening of amino acid isomerases.

Gavina JM, White CE, Finan TM, Britz-McKibbin P
Electrophoresis. 2010; 31: 2831-7

Isomerases involved in the metabolism of D/L-amino acids represent promising therapeutic targets for treatment of disease. Herein, we report a tunable platform for the assessment of enzymatic kinetics involving amino acid isomerization by CE that offers improved selectivity and sensitivity over traditional methods. Enzyme activity and competition assays were evaluated for various hydroxyproline diastereoisomers, proline enantiomers and their structural analogs using 4-hydroxyproline-2-epimerase as a model system. In this work, pyrrole 2-carboxylic acid was found to be a selective inhibitor of 4-hydroxyproline-2-epimerase with a half-maximal inhibition concentration of (2.3 + or - 0.1) mM. Reliable methods for unambiguous characterization of amino acid isomerases are required for the screening of novel inhibitors with epimerase and/or racemase activity.

Molecular cloning of a novel glucuronokinase/putative pyrophosphorylase from zebrafish acting in an UDP-glucuronic acid salvage pathway.

Gangl R, Behmuller R, Tenhaken R
PLoS One. 2014; 9: 89690-89690

In animals, the main precursor for glycosaminoglycan and furthermore proteoglycan biosynthesis, like hyaluronic acid, is UDP-glucuronic acid, which is synthesized via the nucleotide sugar oxidation pathway. Mutations in this pathway cause severe developmental defects (deficiency in the initiation of heart valve formation). In plants, UDP-glucuronic acid is synthesized via two independent pathways. Beside the nucleotide sugar oxidation pathway, a second minor route to UDP-glucuronic acid exist termed the myo-inositol oxygenation pathway. Within this myo-inositol is ring cleaved into glucuronic acid, which is subsequently converted to UDP-glucuronic acid by glucuronokinase and UDP-sugar pyrophosphorylase. Here we report on a similar, but bifunctional enzyme from zebrafish (Danio rerio) which has glucuronokinase/putative pyrophosphorylase activity. The enzyme can convert glucuronic acid into UDP-glucuronic acid, required for completion of the alternative pathway to UDP-glucuronic acid via myo-inositol and thus establishes a so far unknown second route to UDP-glucuronic acid in animals. Glucuronokinase from zebrafish is a member of the GHMP-kinase superfamily having unique substrate specificity for glucuronic acid with a Km of 31 +/- 8 microM and accepting ATP as the only phosphate donor (Km: 59 +/- 9 microM). UDP-glucuronic acid pyrophosphorylase from zebrafish has homology to bacterial nucleotidyltransferases and requires UTP as nucleosid diphosphate donor. Genes for bifunctional glucuronokinase and putative UDP-glucuronic acid pyrophosphorylase are conserved among some groups of lower animals, including fishes, frogs, tunicates, and polychaeta, but are absent from mammals. The existence of a second pathway for UDP-glucuronic acid biosynthesis in zebrafish likely explains some previous contradictory finding in jekyll/ugdh zebrafish developmental mutants, which showed residual glycosaminoglycans and proteoglycans in knockout mutants of UDP-glucose dehydrogenase.

Uridine diphosphate glucuronic acid production and utilization in various tissues actively synthesizing glycosaminoglycans.

Gainey PA, Phelps CF
Biochem J. 1972; 128: 215-27

1. UDP-glucose dehydrogenase has been partially purified from sheep nasal septum cartilage, neonatal rat skin and bovine corneal epithelium. 2. The pH profile, K(m) values for NAD(+) and UDP-glucose, activation energy and molecular weight have been determined for the enzyme from several of the tissues. 3. The sugar nucleotide concentrations in each of the tissues have been related to the spectrum of glycosaminoglycans produced by each tissue. 4. The presence of an allosteric UDP-xylose-binding site distinct from the active site(s) in sheep nasal septum UDP-glucose dehydrogenase has been demonstrated. 5. An active UDP-glucuronic acid nucleotidase has been demonstrated in sheep nasal cartilage. 6. Tissue-space experiments have shown the cell water content of sheep nasal septum cartilage to be 14% of the wet weight. 7. Glucuronic acid 1-phosphate does not occur in measurable amounts in sheep nasal septum cartilage and no UDP-glucuronic acid pyrophosphorylase activity could be detected in this tissue. 8. The inhibition by UDP-xylose with respect to both substrates, UDP-glucose and NAD(+), has been examined, and shown to be allosteric.

Resonance energy transfer between catalytic sites of bovine liver uridine diphosphoglucose dehydrogenase.

Franzen JS, Marchetti PS, Feingold DS
Biochemistry. 1980; 19: 6080-9

A study of the reaction catalysed by alginate lyase VI from the sea mollusc, Littorina sp.

Favorov VV, Vozhova EI, Denisenko VA, Elyakova LA
Biochim Biophys Acta. 1979; 569: 259-66

The molecular weight of polymeric alginic acid digested by alginate lyase (poly(1,4-beta-D-mannuronide) lyase, EC 4.2.2.3) was determined at various stages of the lysis. Low molecular weigh fragments were detected only after 60-100% lysis. Some high molecular weight fragments remained intact even after addition of a fresh aliquot of enzyme to the digest. The enzyme showed maximal activity at pH 5.6 in 0.05 M salt. Enzyme activity was stimulated by addition of 7.5 mM CaCl2 and 0.2 M NaCl, when the pH optimum was between 8 and 8.5. Only mannuronic acid was detected at the reducing end of fragments after exhausive enzymolysis, reduction and hydrolysis. On studying the reaction products by NMR, a double-bound signal (sigma = 5.98 ppm) was observed. A considerable decrease in intensity of the D-mannuronic acid residue signal was detected after hydrolysis of alginate lyase VI on poly-(ManUA-GulUA), but not poly(GulUA). The results suggest that alginate lyase VI may be an endoalginate lyase that splits glycoside bonds only between two mannuronic acid residues.

An approach to the in vitro study of the UTP/UDPglucose/UDP moiety-conserved cycle.

Fassy F, Hervagault JF
Biochim Biophys Acta. 1994; 1200: 297-306

The kinetic behavior of a moiety-conserved ternary cycle is tested experimentally. This system contains the enzymes UDPglucose pyrophosphorylase, glycogen synthase and nucleoside diphosphokinase, converting respectively UTP into UDPglucose, then into UDP and back to UTP in a cyclic manner. The UDPGlc P2ase and NDPK steps are made irreversible by addition of inorganic pyrophosphatase and phosphocreatine kinase, respectively. In order to predict both the evolution and the steady-state values of the various substrates, a model is derived, which takes into account the actual enzyme rate expressions and parameter values, as determined under our experimental conditions. In that model, the UTP, UDPglucose and UDP are taken as the variables, whereas the total concentration of the substrate pool and the four enzyme maximal activities are chosen as the control parameters. Depending upon the various parameter values, monostability, reversible bistability and irreversible transitions may theoretically occur. However, it turns out that some of these values for which multistability might occur, are not accessible experimentally. Under conditions of monostability, the evolutions of the three substrates as experimentally measured are shown to be in good qualitative and quantitative agreement with the model predictions. The relaxation times between two consecutive steady states when a parameter is varied, are shown to be long-lasting processes (several hours). That such an experimental ternary substrate cycle actually exhibits a low sensitivity to any perturbation, addresses the issue to knowing if the same property is likely to occur in vivo, or, in other words, do large moiety-conserved cycles act as metabolic buffers?

Investigation of the UDP-glucose dehydrogenase reaction for a coupled assay of UDP-glucose pyrophosphorylase activities.

Elling L, Kula MR
Biotechnol Appl Biochem. 1991; 14: 306-16

An optimized coupled enzyme assay for UDP-glucose pyrophosphorylase (EC 2.7.7.9) using UDP-glucose dehydrogenase (EC 1.1.1.22) is presented. This optimized assay was developed by a detailed investigation of the kinetics of the UDP-glucose dehydrogenase reaction. In addition the data provide a basis for the enzymatic synthesis of UDP-glucuronic acid. The results demonstrate that the two binding sites of the dehydrogenase differ since a different modulation of the enzyme activity and stability is observed after preincubation with UDP-glucose or NAD+ at various pH values. This is of general interest for the preparation of assay mixtures where UDP-glucose dehydrogenase is used as an auxiliary enzyme.

UDP-glucose dehydrogenase: structure and function of a potential drug target.

Egger S, Chaikuad A, Kavanagh KL, Oppermann U, Nidetzky B
Biochem Soc Trans. 2010; 38: 1378-85

Biosynthesis of the glycosaminoglycan precursor UDP-alpha-D-glucuronic acid occurs through a 2-fold oxidation of UDP-alpha-D-glucose that is catalysed by UGDH (UDP-alpha-D-glucose 6-dehydrogenase). Structure-function relationships for UGDH and proposals for the enzymatic reaction mechanism are reviewed in the present paper, and structure-based sequence comparison is used for subclassification of UGDH family members. The eukaryotic group of enzymes (UGDH-II) utilize an extended C-terminal domain for the formation of complex homohexameric assemblies. The comparably simpler oligomerization behaviour of the prokaryotic group of enzymes (UGDH-I), in which dimeric forms prevail, is traced back to the lack of relevant intersubunit contacts and trimmings within the C-terminal region. The active site of UGDH contains a highly conserved cysteine residue, which plays a key role in covalent catalysis. Elevated glycosaminoglycan formation is implicated in a variety of human diseases, including the progression of tumours. The inhibition of synthesis of UDP-alpha-D-glucuronic acid using UGDH antagonists might therefore be a useful strategy for therapy.

Multiple unfolded states of UDP-galactose 4-epimerase from yeast Kluyveromyces fragilis. Involvement of proline cis-trans isomerization in reactivation.

Dutta S, Maity NR, Bhattacharyya D
Biochim Biophys Acta. 1997; 1343: 251-62

UDP-galactose 4-epimerase from yeast Kluyveromyces fragilis is a dimeric molecule of 75 kDa per subunit with one molecule of cofactor NAD per dimer. It undergoes unfolding and complete dissociation in presence of 8 M urea at pH 7.0 by 10 min. It can be functionally reconstituted almost quantitatively in 2 h by dilution with 20 mM sodium phosphate buffer, pH 7 containing 1 mM extraneous NAD under a second order kinetics [Bhattacharyya, D. (1993) Biochemistry 32, 9726-9734]. Denaturation between 10-60 min inversely affects both the rate and maximum recovery of activity upon refolding. Aggregation of this protein has not been observed under these conditions. The time dependent reaction at the unfolded state is independent of pH between 5.4-10.4 but strongly dependent on temperature of denaturation between 0-20 degrees C. Unfolding at 0 degrees C divides the protein largely into two populations-34% of fast folding species following an apparent first order kinetics and 59% of slow folding species following a second order kinetics of reactivation. A very fast folding species of low abundance 3.5-7.5% depending on temperature of denaturation has been identified, which gets active status within the dead time of mixing. Interaction with the active site directed fluorescence probe 1-anilino 8-naphthalene sulfonic acid (1-ANS) and estimation of bound NAD suggest that the catalytic region of this enzyme is not formed in the long term denatured samples. The whole process of reactivation is catalysed by peptidyl prolyl cis-trans isomerase and thus suggests that one or more proline residues stereochemically control the rate limiting step of reactivation.

Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosadagger.

Du Q, Tian J, Yang X, Pan W, Xu B, Li B, Ingvarsson PK, Zhang D
DNA Res. 2015; 22: 53-67

Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q </= 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.

Interaction of uridine diphosphate glucose with calf liver uridine diphosphate glucose dehydrogenase. Significance of hydroxyl groups at C-3, C-4 and C-6 of hexosyl residue.

Druzhinina TN, Kusov YY, Shibaev VN, Kochetkov NK
Biochim Biophys Acta. 1975; 403: 1-8

Analogs of uridine diphosphate glucose (UDPGlc) with a modified hexosyl residue which contained a deoxy-unit at C-3 or C-4 were tested as substrates of calf liver UDPGlc dehydrogenase (EC 1.1.1.22). The 3-deoxyglucose derivative was found not to serve as a substrate for the enzyme whereas the 4-deoxyglucose analog was able to participate in the reaction. The apparent Km of the latter was 5.3 times that of UDPGlc and the relative V was 0.04. The reaction product was identified as uridine diphosphate deoxyhexuronic acid. UDP-deoxyhexoses were non-competitive inhibitors of UDPGlc enzymic oxidation, inhibition increased in the sequence: 2-deoxy-less than 3-and 6-deoxy-less than 4-deoxyglucose derivative. The significance of different HO-groups in hexosyl residue for interaction of UDPGlc with the enzyme is discussed.

Nucleotide sequence and expression of the algE gene involved in alginate biosynthesis by Pseudomonas aeruginosa.

Chu L, May TB, Chakrabarty AM, Misra TK
Gene. 1991; 107: 1-10

Alginate (Alg), a random polymer of mannuronic acid and glucuronic acid residues, is synthesized and secreted by Pseudomonas aeruginosa primarily during its infection of the lungs of cystic fibrosis patients. The molecular biology and biochemistry of the enzymatic steps leading to the production of the Alg precursor GDP-mannuronic acid have been elucidated, but the mechanism of polymer formation and export of Alg are not understood. We report the nucleotide sequence of a 2.4-kb DNA fragment containing the algE gene, previously designated alg76, encoding the AlgE protein (Mr 54,361) that is believed to be involved in these late steps of Alg biosynthesis. Expression of algE appears to occur from its own promoter. The promoter region contains several direct and inverted repeat sequences and shares structural similarity with promoters of several other alg genes from P. aeruginosa. In addition, the AlgE protein was overproduced from the tac promoter in P. aeruginosa. N-terminal amino acid sequence analysis showed that the polypeptide contains a signal peptide which is cleaved to form the mature protein during AlgE export from the cell cytoplasm.

Monometoxytrityl derivatives of uridine as inhibitors of a human recombinant UDP-glucuronosyltransferase: UGT1*6.

Cano V, Lorentz C, Magdalou J, Loppinet V, Siest G, Ziegler JC
Life Sci. 1997; 61: 18-18

A series of inhibitors of the human liver recombinant UDP-glucuronosyltransferase 1*6 derived from uridine were synthetized as probes of the binding site of the cosubstrate, UDP-glucuronic acid. If triphenylmethanol or uridine alone failed to inhibit the glucuronidation of 4-methylumbelliferone, the trityl derivatives of uridine were found to be very effective inhibitors of the enzyme (Ki 4.4 to 73 microM). The type of inhibition (competitive or mixed) varied with the substitutions on the uracile or on the triphenylmethyl moiety by halogen atoms or methyl groups. Structural features for the binding of the cofactor are postulated.

The structure of UDP-N-acetylglucosamine 2-epimerase reveals homology to phosphoglycosyl transferases.

Campbell RE, Mosimann SC, Tanner ME, Strynadka NC
Biochemistry. 2000; 39: 14993-5001

Bacterial UDP-N-acetylglucosamine 2-epimerase catalyzes the reversible epimerization at C-2 of UDP-N-acetylglucosamine (UDP-GlcNAc) and thereby provides bacteria with UDP-N-acetylmannosamine (UDP-ManNAc), the activated donor of ManNAc residues. ManNAc is critical for several processes in bacteria, including formation of the antiphagocytic capsular polysaccharide of pathogens such as Streptococcus pneumoniae types 19F and 19A. We have determined the X-ray structure (2.5 A) of UDP-GlcNAc 2-epimerase with bound UDP and identified a previously unsuspected structural homology with the enzymes glycogen phosphorylase and T4 phage beta-glucosyltransferase. The relationship to these phosphoglycosyl transferases is very intriguing in terms of possible similarities in the catalytic mechanisms. Specifically, this observation is consistent with the proposal that the UDP-GlcNAc 2-epimerase-catalyzed elimination and re-addition of UDP to the glycal intermediate may proceed through a transition state with significant oxocarbenium ion-like character. The homodimeric epimerase is composed of two similar alpha/beta/alpha sandwich domains with the active site located in the deep cleft at the domain interface. Comparison of the multiple copies in the asymmetric unit has revealed that the epimerase can undergo a 10 degrees interdomain rotation that is implicated in the regulatory mechanism. A structure-based sequence alignment has identified several basic residues in the active site that may be involved in the proton transfer at C-2 or stabilization of the proposed oxocarbenium ion-like transition state. This insight into the structure of the bacterial epimerase is applicable to the homologous N-terminal domain of the bifunctional mammalian UDP-GlcNAc "hydrolyzing" 2-epimerase/ManNAc kinase that catalyzes the rate-determining step in the sialic acid biosynthetic pathway.

A microassay for UDP-glucose dehydrogenase.

Burrows RB, Cintron C
Anal Biochem. 1983; 130: 376-8

An assay for UDP-glucuronic acid [J. Singh, L. R. Schwarz, and F. J. Wiebel, Biochem. J. 189, 369-372 (1980)] has been utilized for determining UDP-glucose dehydrogenase activity. The assay for UDP-glucuronic acid, a product of UDP-glucose dehydrogenase, is based on the fluorometric determination of D-glucuronosyl benzo(a)pyrene. This compound is formed from UDP-glucuronic acid and 3-hydroxybenzo(a)pyrene in a reaction catalyzed by the glycuronosyl transferase of guinea pig microsomes. Unreacted 3-hydroxybenzo(a)pyrene is removed by extraction with chloroform-methanol, and the amount of gluconosylbenzo(a)pyrene formed is determined fluorometrically. Because this assay for UDP-glucose dehydrogenase is about 500 times more sensitive than spectrophotometric assays, it can be used to measure the amount of enzyme extractable from milligram quantities of connective tissue. Some kinetic properties of UDP-glucose dehydrogenase extracted from rabbit tissue have been determined. No evidence of different forms of the enzyme in rabbit liver, cartilage, or corneal stroma was found.

Patterns of product inhibition of a bifunctional dehydrogenase; L-histidinol:NAD+ oxidoreductase.

Burger E, Gorisch H
Eur J Biochem. 1981; 116: 137-42

The steady-state kinetic patterns of the bifunctional enzyme histidinol dehydrogenase from Salmonella typhimurium (EC 1.1.1.23) are compatible with a bi-uni uni-bi ping-pong mechanism. Studies of product inhibition make it possible to determine the sequence of substrate binding and product dissociation. Histidinol binds first to the enzyme, followed by the binding of NAD+; histidine is the last product to dissociate from histidinol dehydrogenase. Five of ten kinetic constants defined are determined from linear intercept and slope replots; Km for histidinol was found to be 16 +/- 3 microM and for NAD+ 1 +/- 0.3 mM; K2 for NAD+ was determined to be 0.8 +/- 0.4 mM and K3 for NADH to be 0.3 +/- 0.07 mM. K1 for histidine was found to be 2.1 +/- 0.5 mM.

Characterisation and expression of the pathway from UDP-glucose to UDP-xylose in differentiating tobacco tissue.

Bindschedler LV, Wheatley E, Gay E, Cole J, Cottage A, Bolwell GP
Plant Mol Biol. 2005; 57: 285-301

The pathway from UDP-glucose to UDP-xylose has been characterised in differentiating tobacco tissue. A xylogenic suspension cell culture of tobacco has been used as a source for the purification of the enzymes responsible for the oxidation of UDP-glucose to UDP-glucuronic acid and its subsequent decarboxylation to UDP-xylose. Protein purification and transcriptional studies show that two possible candidates can contribute to the first reaction. Most of the enzyme activity in the cultured cells could be accounted for by a protein with an Mr of 43 kDa which had dual specificity for UDP-glucose and ethanol. The cognate cDNA, with similarity to alcohol dehydrogenases (NtADH2) was expressed in E. coli to confirm the dual specificity. A second UDP-glucose dehydrogenase, corresponding to the monospecific form, ubiquitous amongst plants and animals, could not be purified from the tobacco cell cultures. However, two cDNAs were cloned with high similarity to the family of UDP-glucose dehydrogenases. Transcripts of both types of dehydrogenase showed highest expression in tissues undergoing secondary wall synthesis. The UDP-glucuronate decarboxylase was purified as polypeptides of Mr 87 and 40 kDa. Peptide fingerprinting of the latter polypeptide identified it as a form of UDP-glucuronate decarboxylase and functionality was established by expressing the cognate cDNA in E. coli. Expression of 40 kDa polypeptide and its corresponding mRNA was also found to be highest in tissues associated with secondary wall formation.

Conformationally vicinal thiols of UDP-glucose-4-epimerase from Saccharomyces fragilis: selective roles in maintaining coenzyme fluorescence and activity.

Bhattacharjee H, Bhaduri A
Indian J Biochem Biophys. 1988; 25: 660-3

Identification and characterization of AlgZ, an AlgT-dependent DNA-binding protein required for Pseudomonas aeruginosa algD transcription.

Baynham PJ, Wozniak DJ
Mol Microbiol. 1996; 22: 97-108

Transcriptional activation of the Pseudomonas aeruginosa algD gene results in high-level synthesis of the capsular polysaccharide alginate, an important P. aeruginosa virulence factor expressed in cystic fibrosis (CF) patients with chronic pulmonary disease. In this study, electrophoretic mobility-shift assays were used to identify a novel protein (AlgZ), which binds specifically to a sequence located 280 bp upstream of the algD promoter. While AlgZ-binding activity did not require the response regulators AlgB or AlgR, expression of AlgZ was found to be absolutely dependent on the alternative sigma factor AlgT. Electrophoretic mobility-shift assays and copper-phenanthroline footprinting localized AlgZ binding to a 36 bp algD region, which includes several helical repeats. A collection of alginate-producing (mucoid) and non-mucoid P. aeruginosa strains, derived from CF patients, was characterized for AlgZ-binding activity. In all cases, AlgZ binding to algD sequences was observed when extracts derived from mucoid P. aeruginosa CF isolates were examined. However, this binding activity was not present when extracts from non-mucoid P. aeruginosa CF isolates were tested. Oligonucleotide mutagenesis was employed to create an algD allele with a 4 bp mutation in the predicted AlgZ-binding site (algD38) and a heterologous substitution allele (algD40), in which the entire AlgZ-binding site was replaced with a non-specific DNA sequence of identical size. When the algD38 mutation was cloned into an algD-cat transcriptional fusion, this resulted in a 28-fold reduction in algD expression, whereas the algD40 mutation abolished algD transcription, indicating that AlgZ acts as an activator of algD transcription. These results support the hypothesis that activation of algD involves the formation of a high-order looped structure allowing for multivalent contacts between AlgZ, AlgR and RNA polymerase containing the alternative sigma factor AlgT. Characterization of the molecular details of algD activation will provide insights into the control of other prokaryotic and eukaryotic promoters that utilize multiple activators.

Inhibition of uridine diphosphoglucose dehydrogenase by galactosamine-I-phosphate and UDP-galactosamine.

Bauer C, Reutter W
Biochim Biophys Acta. 1973; 293: 11-4

Allohydroxy-D-proline dehydrogenase. An inducible membrane-bound enzyme in Pseudomonas aeruginosa PA01.

Bater AJ, Venables WA, Thomas S
Arch Microbiol. 1977; 112: 287-9

Growth of Pseudomonas aeruginosa PA01 on isomers of hydroxyproline induced the synthesis of an allohydroxy-D-proline dehydrogenase. The enzyme resembled the D-alanine dehydrogenase of this organism in its association with the particulate fraction and its linkage to oxygen through a cytochrome-containing respiratory chain, but differed from this and other bacterial D-amino acid dehydrogenases in its high substrate specificity and low Km.

Biosynthesis of uridine diphosphate D-xylose. 3. Uridine diphosphate D-glucose dehydrogenase of Cryptococcus laurentii.

Ankel H, Ankel E, Feingold DS
Biochemistry. 1966; 5: 1864-9