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| | <StructureSection load='7vdy' size='340' side='right'caption='[[7vdy]], [[Resolution|resolution]] 2.12Å' scene=''> | | <StructureSection load='7vdy' size='340' side='right'caption='[[7vdy]], [[Resolution|resolution]] 2.12Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7vdy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VDY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7vdy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lavendulae Streptomyces lavendulae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VDY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.12Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/O-ureido-serine_racemase O-ureido-serine racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.19 5.1.1.19] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=7vdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vdy OCA], [https://pdbe.org/7vdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vdy RCSB], [https://www.ebi.ac.uk/pdbsum/7vdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vdy 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=7vdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vdy OCA], [https://pdbe.org/7vdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vdy RCSB], [https://www.ebi.ac.uk/pdbsum/7vdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vdy ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DCSC_STRLA DCSC_STRLA]] Involved in the biosynthesis of the antibiotic D-cycloserine (DCS), a cyclic structural analog of D-alanine, used as an antitubercular agent. Catalyzes the stereoinversion of O-ureido-L-serine to O-ureido-D-serine.<ref>PMID:20086163</ref> <ref>PMID:22307920</ref> <ref>PMID:23529730</ref>
| + | [https://www.uniprot.org/uniprot/DCSC_STRLA DCSC_STRLA] Involved in the biosynthesis of the antibiotic D-cycloserine (DCS), a cyclic structural analog of D-alanine, used as an antitubercular agent. Catalyzes the stereoinversion of O-ureido-L-serine to O-ureido-D-serine.<ref>PMID:20086163</ref> <ref>PMID:22307920</ref> <ref>PMID:23529730</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: O-ureido-serine racemase]] | + | [[Category: Streptomyces lavendulae]] |
| - | [[Category: Matoba, Y]] | + | [[Category: Matoba Y]] |
| - | [[Category: Oda, K]] | + | [[Category: Oda K]] |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Racemase]]
| + | |
| Structural highlights
Function
DCSC_STRLA Involved in the biosynthesis of the antibiotic D-cycloserine (DCS), a cyclic structural analog of D-alanine, used as an antitubercular agent. Catalyzes the stereoinversion of O-ureido-L-serine to O-ureido-D-serine.[1] [2] [3]
Publication Abstract from PubMed
The O-ureidoserine racemase (DcsC) is an enzyme found from the biosynthetic gene cluster of antitubercular agent d-cycloserine. Although DcsC is homologous to diaminopimelate epimerase (DapF) that catalyzes the interconversion between ll- and dl-diaminopimelic acid, it specifically catalyzes the interconversion between O-ureido-l-serine and its enantiomer. Here we determined the crystal structure of DcsC at a resolution of 2.12 A, implicating that the catalytic mechanism of DcsC shares similarity with that of DapF. Comparing the structure of the active center of DcsC to that of DapF, Thr72, Thr198, and Tyr219 of DcsC are likely to be involved in the substrate specificity.
Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway.,Oda K, Sakaguchi T, Matoba Y Proteins. 2022 Apr;90(4):912-918. doi: 10.1002/prot.26290. Epub 2021 Dec 17. PMID:34877716[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kumagai T, Koyama Y, Oda K, Noda M, Matoba Y, Sugiyama M. Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Antimicrob Agents Chemother. 2010 Mar;54(3):1132-9. doi: 10.1128/AAC.01226-09., Epub 2010 Jan 19. PMID:20086163 doi:http://dx.doi.org/10.1128/AAC.01226-09
- ↑ Dietrich D, van Belkum MJ, Vederas JC. Characterization of DcsC, a PLP-independent racemase involved in the biosynthesis of D-cycloserine. Org Biomol Chem. 2012 Mar 21;10(11):2248-54. doi: 10.1039/c2ob06864h. Epub 2012, Feb 6. PMID:22307920 doi:http://dx.doi.org/10.1039/c2ob06864h
- ↑ Uda N, Matoba Y, Kumagai T, Oda K, Noda M, Sugiyama M. Establishment of an in vitro D-cycloserine-synthesizing system by using O-ureido-L-serine synthase and D-cycloserine synthetase found in the biosynthetic pathway. Antimicrob Agents Chemother. 2013 Jun;57(6):2603-12. doi: 10.1128/AAC.02291-12., Epub 2013 Mar 25. PMID:23529730 doi:http://dx.doi.org/10.1128/AAC.02291-12
- ↑ Oda K, Sakaguchi T, Matoba Y. Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway. Proteins. 2022 Apr;90(4):912-918. doi: 10.1002/prot.26290. Epub 2021 Dec 17. PMID:34877716 doi:http://dx.doi.org/10.1002/prot.26290
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