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| | <StructureSection load='1sbr' size='340' side='right'caption='[[1sbr]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='1sbr' size='340' side='right'caption='[[1sbr]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1sbr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SBR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1sbr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SBR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=VIB:3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM'>VIB</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=VIB:3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM'>VIB</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s99|1s99]], [[1lxj|1lxj]], [[1lxn|1lxn]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YkoF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
| + | |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sbr OCA], [https://pdbe.org/1sbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sbr RCSB], [https://www.ebi.ac.uk/pdbsum/1sbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sbr ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sbr OCA], [https://pdbe.org/1sbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sbr RCSB], [https://www.ebi.ac.uk/pdbsum/1sbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sbr ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/YKOF_BACSU YKOF_BACSU]] Part of the ABC transporter complex YkoCDEF that could transport hydroxymethylpyrimidine (HMP) and/or thiamine. Could also transport other HMP-containing products. Binds thiamine via its HMP moiety.<ref>PMID:12376536</ref> <ref>PMID:16291685</ref>
| + | [https://www.uniprot.org/uniprot/YKOF_BACSU YKOF_BACSU] Part of the ABC transporter complex YkoCDEF that could transport hydroxymethylpyrimidine (HMP) and/or thiamine. Could also transport other HMP-containing products. Binds thiamine via its HMP moiety.<ref>PMID:12376536</ref> <ref>PMID:16291685</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Derewenda, U]] | + | [[Category: Derewenda U]] |
| - | [[Category: Derewenda, Z S]] | + | [[Category: Derewenda ZS]] |
| - | [[Category: Devedjiev, Y]] | + | [[Category: Devedjiev Y]] |
| - | [[Category: Surendranath, Y]] | + | [[Category: Surendranath Y]] |
| - | [[Category: Act-domain family]]
| + | |
| - | [[Category: Ligand binding protein]]
| + | |
| - | [[Category: Thiamin-binding protein]]
| + | |
| - | [[Category: Ykof]]
| + | |
| Structural highlights
Function
YKOF_BACSU Part of the ABC transporter complex YkoCDEF that could transport hydroxymethylpyrimidine (HMP) and/or thiamine. Could also transport other HMP-containing products. Binds thiamine via its HMP moiety.[1] [2]
Publication Abstract from PubMed
The crystal structure of the Bacillus subtilis YkoF gene product, a protein involved in the hydroxymethyl pyrimidine (HMP) salvage pathway, was solved by the multiwavelength anomalous dispersion (MAD) method and refined with data extending to 1.65 A resolution. The atomic model of the protein shows a homodimeric association of two polypeptide chains, each containing an internal repeat of a ferredoxin-like betaalphabetabetaalphabeta fold, as seen in the ACT and RAM-domains. Each repeat shows a remarkable similarity to two members of the COG0011 domain family, the MTH1187 and YBL001c proteins, the crystal structures of which were recently solved by the Northeast Structural Genomics Consortium. Two YkoF monomers form a tightly associated dimer, in which the amino acid residues forming the interface are conserved among family members. A putative small-ligand binding site was located within each repeat in a position analogous to the serine-binding site of the ACT-domain of the Escherichia coli phosphoglycerate dehydrogenase. Genetic data suggested that this could be a thiamin or HMP-binding site. Calorimetric data confirmed that YkoF binds two thiamin molecules with varying affinities and a thiamine-YkoF complex was obtained by co-crystallization. The atomic model of the complex was refined using data to 2.3 A resolution and revealed a unique H-bonding pattern that constitutes the molecular basis of specificity for the HMP moiety of thiamin.
The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins.,Devedjiev Y, Surendranath Y, Derewenda U, Gabrys A, Cooper DR, Zhang RG, Lezondra L, Joachimiak A, Derewenda ZS J Mol Biol. 2004 Oct 15;343(2):395-406. PMID:15451668[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem. 2002 Dec 13;277(50):48949-59. Epub 2002 Oct 9. PMID:12376536 doi:http://dx.doi.org/10.1074/jbc.M208965200
- ↑ Schyns G, Potot S, Geng Y, Barbosa TM, Henriques A, Perkins JB. Isolation and characterization of new thiamine-deregulated mutants of Bacillus subtilis. J Bacteriol. 2005 Dec;187(23):8127-36. PMID:16291685 doi:http://dx.doi.org/187/23/8127
- ↑ Devedjiev Y, Surendranath Y, Derewenda U, Gabrys A, Cooper DR, Zhang RG, Lezondra L, Joachimiak A, Derewenda ZS. The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins. J Mol Biol. 2004 Oct 15;343(2):395-406. PMID:15451668 doi:10.1016/j.jmb.2004.08.037
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