NORMAL GENOMIC

• Chakraborty R, Lemke EA, Cao Z, Klebba PE, van der Helm D
• Identification and mutational studies of conserved amino acids in theouter membrane receptor protein, FepA, which affect transport but notbinding of ferric-enterobactin in Escherichia coli.
• Biometals. 2003; 16: 507-18
• Display abstract

• Many gram-negative bacteria produce and excrete siderophores, whichcomplex iron with high affinity in the environment. The ferric siderophorecomplexes are transported across the outer membrane by receptor proteins.This process requires energy and is TonB dependent and must involveconformational changes in the receptor proteins to allow the transport ofthe ferric siderophores from the extracellular binding site to theperiplasm. There is a large variety in the structures, molecular weightsand charges among the siderophores. It was therefore realized that whenthe sequences of the many different receptor proteins were compared,simultaneously, all identities and close similarities, found in thismanner, could only be due to residues involved in the conformationalchanges and transport mechanism, common to all the proteins, and not bedue to the specificity of ligand recognition. Once the crystal structuresof FepA, FhuA and FecA became available, it was immediately clear that thesequence similarities which were found in the simultaneous alignment, wereall localized in a few structural domains, which are identical in thethree structures and can therefore be expected to be maintained in all theproteins in this family. One of these domains, tentatively named the lockregion, consists of 10 residues with a central quadrupole formed by twoarginines and two glutamates, from the plug region and the beta barrel. Wemutated several of these residues in FepA. All showed normal binding inquantitative binding studies. Some showed normal transport as well,however, the majority showed moderate to severe defective transport withferric enterobactin. The results therefore show the validity of thehypothesis that the simultaneous sequence alignment will select theresidues involved in the transport function of the receptor proteins. Inaddition the results allow to relate the severity of the transportdeficiency to be correlated with the structure of the lock region while itis also possible to propose a function of this region in theconformational changes of the protein during the transport of the ligandfrom the binding site to the periplasm.

• Cornelis P, Matthijs S
• Diversity of siderophore-mediated iron uptake systems in fluorescentpseudomonads: not only pyoverdines.
• Environ Microbiol. 2002; 4: 787-98
• Display abstract

• Fluorescent pseudomonads are gamma-proteobacteria known for their capacityto colonize various ecological niches. This adaptability is reflected bytheir sophisticated and diverse iron uptake systems. The majority offluorescent pseudomonads produce complex peptidic siderophores calledpyoverdines or pseudobactins, which are very efficient iron scavengers. Atremendous variety of pyoverdines has been observed, each speciesproducing a different pyoverdine. This variety can be used as aninteresting tool to study the diversity and taxonomy of fluorescentpseudomonads. Other siderophores, including newly described ones, are alsoproduced by pseudomonads, sometimes endowed with interesting properties inaddition to iron scavenging, such as formation of complexes with othermetals or antimicrobial activity. Factors other than iron limitation, anddifferent regulatory proteins also seem to influence the production ofsiderophores in pseudomonads and are reviewed here as well. Anotherpeculiarity of pseudomonads is their ability to use a large number ofheterologous siderophores via different TonB-dependent receptors. A firstgenomic analysis of receptors in four different fluorescent pseudomonadssuggests that their siderophore ligand repertoire is likely to overlap,and that not all receptors recognize siderophores as ligands.

• Rabsch W, Voigt W, Reissbrodt R, Tsolis RM, Baumler AJ
• Salmonella typhimurium IroN and FepA proteins mediate uptake ofenterobactin but differ in their specificity for other siderophores.
• J Bacteriol. 1999; 181: 3610-2
• Display abstract

• Salmonella typhimurium possesses two outer membrane receptor proteins,IroN and FepA, which have been implicated in the uptake of enterobactin.To determine whether both receptors have identical substratespecificities, fepA and iroN mutants and a double mutant werecharacterized. While both receptors transported enterobactin, the uptakeof corynebactin and myxochelin C was selectively mediated by IroN andFepA, respectively.

• Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R
• Antibacterial activity in bovine lactoferrin-derived peptides.
• Antimicrob Agents Chemother. 1997; 41: 54-9
• Display abstract

• Several peptides sharing high sequence homology with lactoferricin B(Lf-cin B) were generated from bovine lactoferrin (Lf) with recombinantchymosin. Two peptides were copurified, one identical to Lf-cin B andanother differing from Lf-cin B by the inclusion of a C-terminal alanine(lactoferricin). Two other peptides were copurified fromchymosin-hydrolyzed Lf, one differing from Lf-cin B by the inclusion ofC-terminal alanyl-leucine and the other being a heterodimer linked by adisulfide bond. These peptides were isolated in a single step fromchymosin-hydrolyzed Lf by membrane ion-exchange chromatography and werepurified by reverse-phase high-pressure liquid chromatography (HPLC). Theywere characterized by N-terminal Edman sequencing, mass spectrometry, andantibacterial activity determination. Pure lactoferricin, prepared frompepsin-hydrolyzed Lf, was purified by standard chromatography techniques.This peptide was analyzed against a number of gram-positive andgram-negative bacteria before and after reduction of its disulfide bond orcleavage after its single methionine residue and was found to inhibit thegrowth of all the test bacteria at a concentration of 8 microM or less.Subfragments of lactoferricin were isolated from reduced and cleavedpeptide by reverse-phase HPLC. Subfragment 1 (residues 1 to 10) was activeagainst most of the test microorganisms at concentrations of 10 to 50microM. Subfragment 2 (residues 11 to 26) was active against only a fewmicroorganisms at concentrations up to 100 microM. These antibacterialstudies indicate that the activity of lactoferricin is mainly, but notwholly, due to its N-terminal region.

• Xiong J, Subramaniam S, Govindjee
• Modeling of the D1/D2 proteins and cofactors of the photosystem IIreaction center: implications for herbicide and bicarbonate binding.
• Protein Sci. 1996; 5: 2054-73
• Display abstract

• A three-dimensional model of the photosystem II (PSII) reaction centerfrom the cyanobacterium Synechocystis sp. PCC 6803 was generated based onhomology with the anoxygenic purple bacterial photosynthetic reactioncenters of Rhodobacter sphaeroides and Rhodopseudomonas viridis, for whichthe X-ray crystallographic structures are available. The model wasconstructed with an alignment of D1 and D2 sequences with the L and Msubunits of the bacterial reaction center, respectively, and by using as ascaffold the structurally conserved regions (SCRs) from bacterialtemplates. The structurally variant regions were built using a novelsequence-specific approach of searching for the best-matched proteinsegments in the Protein Data Bank with the "basic local alignment searchtool" (Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, 1990, J MolBiol 215:403-410), and imposing the matching conformational preference onthe corresponding D1 and D2 regions. The structure thus obtained wasrefined by energy minimization. The modeled D1 and D2 proteins containfive transmembrane alpha-helices each, with cofactors (4 chlorophylls, 2pheophytins, 2 plastoquinones, and a non-heme iron) essential for PSIIprimary photochemistry embedded in them. A beta-carotene, consideredimportant for PSII photoprotection, was also included in the model. Fourdifferent possible conformations of the primary electron donor P680chlorophylls were proposed, one based on the homology with the bacterialtemplate and the other three on existing experimental suggestions inliterature. The P680 conformation based on homology was preferred becauseit has the lowest energy. Redox active tyrosine residues important forP680+ reduction as well as residues important for PSII cofactor bindingwere analyzed. Residues involved in interprotein interactions in the modelwere also identified. Herbicide 3-(3,4-dichlorophenyl)-1,1-dimethylurea(DCMU) was also modeled in the plastoquinone QB binding niche using thestructural information available from a DCMU-binding bacterial reactioncenter. A bicarbonate anion, known to play a role in PSII, but not inanoxygenic photosynthetic bacteria, was modeled in the non-heme iron site,providing a bidentate ligand to the iron. By modifying the previoushypothesis of Blubaugh and Govindjee (1988, Photosyn Res 19:85-128), wemodeled a second bicarbonate and a water molecule in the QB site and weproposed a hypothesis to explain the mechanism of QB protonation mediatedby bicarbonate and water. The bicarbonate, stabilized by D1-R257, donatesa proton to QB2- through the intermediate of D1-H252; and a water moleculedonates another proton to QB2-. Based on the discovery of a "watertransport channel" in the bacterial reaction center, an analogous channelfor transporting water and bicarbonate is proposed in our PSII model. Theputative channel appears to be primarily positively charged near QB andthe non-heme iron, in contrast to the polarity distribution in thebacterial water transport channel. The constructed model has been found tobe consistent with most existing data.

• Brodie AM, Ainscough EW, Baker EN, Baker HM, Shongwe MS, Smith CA
• Synergism and substitution in the lactoferrins.
• Adv Exp Med Biol. 1994; 357: 33-44
• Display abstract

• The anion binding properties of human lactoferrin (Lf), with Fe3+ or Cu2+as the associated metal ion, highlight differences between the two sites,and in the anion binding behaviour when different metals are bound.Carbonate, oxalate and hybrid carbonate-oxalate complexes have beenprepared and their characteristic electronic and EPR spectra recorded.Oxalate can displace carbonate from either one or both anion sites ofCu2(CO3)2Lf, depending on the oxalate concentration, but no suchdisplacement occurs for Fe2(CO3)2Lf although it does for the bovineanalogue. Addition of oxalate and the appropriate metal ion to apoLf undercarbonate-free conditions gives dioxalate complexes with both Fe3+ andCu2+. The anion sites as determined from the crystal structures ofFe2(CO3)2Lf, Fe2(C2O4)2Lf, Cu2(CO3)2Lf, and Cu2(CO3)(C2O4)Lf have beencompared. Both the carbonate and oxalate ions bind in bidentate fashion tothe metal, except that the carbonate ion in the N-lobe site of dicupriclactoferrin is monodentate. The hybrid copper lactoferrin complex showsthat the oxalate ion binds preferentially in the C-lobe site in abidentate mode. A series of complexes containing the synergistic anionO,N-chelates with increasing substitution on the N atom (glycinate,iminodiacetate and nitrilotriacetate) have been prepared with iron bovinelactoferrin for comparison with the O,O-chelate oxalate. Overall theseobservations lead to a generalised model for synergistic anion binding bytransferrins and allow comparisons to be made with nonsynergistic anionssuch as citrate and succinate.

• Burley SK, David PR, Sweet RM, Taylor A, Lipscomb WN
• Structure determination and refinement of bovine lens leucineaminopeptidase and its complex with bestatin.
• J Mol Biol. 1992; 224: 113-40
• Display abstract

• The three-dimensional structure of bovine lens leucine aminopeptidase (EC3.4.11.1) complexed with bestatin, a slow-binding inhibitor, has beensolved to 3.0 A resolution by the multiple isomorphous replacement methodwith phase combination and density modification. In addition, thisstructure and the structure of the isomorphous native enzyme have beenrefined at 2.25 and 2.32 A resolution, respectively, with crystallographicR-factors of 0.180 and 0.159, respectively. The current structural modelfor the enzyme includes the two zinc ions and 481 of the 487 amino acidresidues comprising the asymmetric unit. The enzyme is physiologicallyactive as a hexamer, which has 32 symmetry, and is triangular in shapewith a triangle edge length of 115 A and maximal thickness of 90 A.Monomers are crystallographically equivalent. Each is folded into twounequal alpha/beta domains connected by an alpha-helix to give acomma-like shape with approximate maximal dimensions of 90 A x 55 A x 55A. The secondary structural composition is 35% alpha-helix and 23%beta-strand. The N-terminal domain (160 amino acid residues) mediatestrimer-trimer interactions and does not appear to participate directly incatalysis, while the C-terminal domain (327 amino acid residues) isresponsible for catalysis and binds the two zinc ions, which are less than3 A apart. These two metal ions are located near the edge of aneight-stranded, saddle-shaped beta-sheet. The zinc ion that has the lowertemperature factor is co-ordinated by one carboxylate oxygen atom fromeach of Asp255, Asp332 and Glu334, and the carbonyl oxygen of Asp332. Theother zinc ion, presumed to be readily exchangeable, is co-ordinated byone carboxylate oxygen atom of each of Asp273 and Glu334 and theside-chain amino group of Lys250. The active site also contains twopositively charged residues, Lys262 and Arg336. The six active sites arethemselves located in the interior of the hexamer, where they line adisk-shaped cavity of radius 15 A and thickness 10 A. Access to thiscavity is provided by solvent channels that run along the 2-fold symmetryaxes. Bestatin binds to one of the active site zinc ions, and itsphenylalanine and leucine side-chains occupy hydrophobic pockets adjacentto the active site. Finally, the relationship between bovine lens leucineaminopeptidase and the homologous enzyme pepA from Escherichia coli isdiscussed.

• Ago H, Kitagawa Y, Fujishima A, Matsuura Y, Katsube Y
• Crystal structure of basic fibroblast growth factor at 1.6 A resolution.
• J Biochem. 1991; 110: 360-3
• Display abstract

• We have determined the crystal structures of two types of human basicfibroblast growth factor, the serine analogue and the wild-type, at 1.6and 2.5 A resolution, respectively. Two good heavy atom derivatives werefound and used for multiple isomorphous replacement phasing. The atomiccoordinates were refined using the Hendrickson & Konnert program forstereochemically restrained refinement against structure factors. Thecrystallographic R factors were reduced to 15.3% for the serine analoguestructure and 16.0% for the wild-type structure. The serine analogue andwild-type structures have been found to be almost identical, theroot-mean-square deviation between the corresponding C alpha atoms being0.11 A. Their structures are composed of twelve beta-strands forming abarrel and three loops. Their molecules have an approximate threefoldinternal symmetry and are similar in architecture to that of interleukin-1beta. A possible heparin-binding site, which comprises five basicresidues, Lys119, Arg120, Lys125, Lys129, and Lys135, has been revealed bycalculating the electrostatic potential energy.

• Stec B, Lebioda L
• Refined structure of yeast apo-enolase at 2.25 A resolution.
• J Mol Biol. 1990; 211: 235-48
• Display abstract

• The crystal structure of apo-enolase from baker's yeast (Saccharomycescerevisiae) was established at 2.25 A resolution using a restrainedleast-squares refinement method. Based on 21,077 independent reflectionsof better than 8 A resolution, a final R-factor of 15.4% was obtained witha model obeying standard geometry within 0.017 A in bond length and 3.5degrees in bond angles. The upper limit for the co-ordinate accuracy ofthe atoms was estimated to be 0.18 A. The refinement confirmed theheterodox, non-parallel character of the 8-fold beta alpha-barrel domainwith beta beta alpha alpha(beta alpha)6 topology. The reported structurefor which the data were collected at pH 5.0 represents an apo-form of theenzyme. Of the three carboxylic ligands that form the conformational metalion binding site two, Glu295 and Asp320, are very close and presumablyform a strong acidic type hydrogen bond with the proton partiallyreplacing the electric charge of the physiological cofactor Mg2+. Thesingle sulfate ion found in the structure is in the active site cavity,co-ordinated to the side-chains of Lys345 and Arg374, and to the N atom ofSer375. It is located about 7.4 A from the conformational metal ionbinding site. It occupies the site in which the phosphate group of thesubstrate binds.

• Brock JH
• Iron and the outcome of infection.
• Br Med J (Clin Res Ed). 1986; 293: 518-20

• Bridges KR, Cudkowicz A
• Effect of iron chelators on the transferrin receptor in K562 cells.
• J Biol Chem. 1984; 259: 12970-7
• Display abstract

• Delivery of iron to K562 cells by diferric transferrin involves a cycle ofbinding to surface receptors, internalization into an acidic compartment,transfer of iron to ferritin, and release of apotransferrin from the cell.To evaluate potential feedback effects of iron on this system, we exposedcells to iron chelators and monitored the activity of the transferrinreceptor. In the present study, we found that chelation of extracellulariron by the hydrophilic chelators desferrioxamine B,diethylenetriaminepentaacetic acid, or apolactoferrin enhanced the releasefrom the cells of previously internalized 125I-transferrin. Presaturationof these compounds with iron blocked this effect. These chelators did notaffect the uptake of iron from transferrin. In contrast, the hydrophobicchelator 2,2-bipyridine, which partitions into cell membranes, completelyblocked iron uptake by chelating the iron during its transfer across themembrane. The 2,2-bipyridine did not, however, enhance the release of125I-transferrin from the cells, indicating that extracellular ironchelation is the key to this effect. Desferrioxamine, unlike the otherhydrophilic chelators, can enter the cell and chelate an intracellularpool of iron. This produced a parallel increase in surface andintracellular transferrin receptors, reaching 2-fold at 24 h and 3-fold at48 h. This increase in receptor number required ongoing protein synthesisand could be blocked by cycloheximide. Diethylenetriaminepentaacetic acidor desferrioxamine presaturated with iron did not induce new transferrinreceptors. The new receptors were functionally active and produced anincrease in 59Fe uptake from 59Fe-transferrin. We conclude that thetransferrin receptor in the K562 cell is regulated in part by chelatableiron: chelation of extracellular iron enhances the release ofapotransferrin from the cell, while chelation of an intracellular ironpool results in the biosynthesis of new receptors.

• Neilands JB
• Siderophores.
• Adv Inorg Biochem. 1983; 5: 137-66

• Hoy TG, Harrison PM, Shabbir M
• Uptake and release of ferritin iron. Surface effects and exchange withinthe crystalline core.
• Biochem J. 1974; 139: 603-7
• Display abstract

• The uptake and subsequent release of iron by apoferritin and ferritin wasstudied by using labelled iron ((59)Fe). The experimental results areconsistent with predictions arising from a model system developed in theinterpretation of previous experiments. In this model, uptake and releaseof ferritin iron is controlled by the available surface area of the smallcrystalline particles of hydrous ferric oxide found within the ferritinmolecule. Evidence is also presented for the exchange of Fe(3+) ions amongthe various cation sites within these crystallites.

• Rieder M
• Zinnwaldite: octahedral ordering in lithium-iron micas.
• Science. 1968; 160: 1338-40
• Display abstract

• Ordering of the octahedral sheet of some lithium-iron micas is proposed onthe basis of chemical compositions and crystallographic properties. Themodel of the ordered sheet has large and small sites in the ratio 2 : 1and explains all observed properties- the small layer thickness, the"dioctahedral reflections," and the n(120 deg) motif in polytypism.