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| | ==Structure of Vibrio cholerae broad spectrum racemase== | | ==Structure of Vibrio cholerae broad spectrum racemase== |
| - | <StructureSection load='4beu' size='340' side='right' caption='[[4beu]], [[Resolution|resolution]] 1.15Å' scene=''> | + | <StructureSection load='4beu' size='340' side='right'caption='[[4beu]], [[Resolution|resolution]] 1.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4beu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BEU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4beu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BEU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 1.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4be4|4be4]], [[4be9|4be9]], [[4beq|4beq]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=4beu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4beu OCA], [https://pdbe.org/4beu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4beu RCSB], [https://www.ebi.ac.uk/pdbsum/4beu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4beu ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4beu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4beu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4beu RCSB], [http://www.ebi.ac.uk/pdbsum/4beu PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/D0H7Y0_VIBCL D0H7Y0_VIBCL]] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids (By similarity).[HAMAP-Rule:MF_01201] | + | [https://www.uniprot.org/uniprot/BSR_VIBCH BSR_VIBCH] Amino-acid racemase able to utilize a broad range of substrates. Reversibly racemizes ten of the 19 natural chiral amino acids known, including both non-beta-branched aliphatic amino acids (Ala, Leu, Met, Ser, Cys, Gln and Asn) and positively charged amino acids (His, Lys and Arg). Among these substrates, is the most efficient with lysine and arginine. Is also able to catalyze the racemization of several amino acids that are not typically incorporated into proteins such as ornithine and norleucine. Is not active on negatively charged (Glu and Asp) or aromatic (Tyr, Trp and Phe) amino acids and displays minimal activity towards beta-branched aliphatic (Ile, Val and Thr) substrates (PubMed:24419381). Enables bacteria to produce and release extracellular non-canonical D-amino acids (NCDAAs) that regulate diverse cellular processes which may function as part of a cooperative strategy in vibrio communities to protect non-producing members from competing bacteria (PubMed:29446806, PubMed:29028003). D-amino acid production by BsrV provides a cue for V.cholerae to decrease peptidoglycan synthesis and to alter its cell wall via incorporation of NCDAAs into the muropeptides, in adaption to stationary phase conditions (PubMed:19762646, PubMed:29028003).<ref>PMID:19762646</ref> <ref>PMID:24419381</ref> <ref>PMID:29028003</ref> <ref>PMID:29446806</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4beu" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Alanine racemase|Alanine racemase]] | + | *[[Alanine racemase 3D structures|Alanine racemase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillo virgola del koch trevisan 1884]] | + | [[Category: Large Structures]] |
| - | [[Category: Alanine racemase]] | + | [[Category: Vibrio cholerae]] |
| - | [[Category: Carrasco-Lopez, C]] | + | [[Category: Carrasco-Lopez C]] |
| - | [[Category: Hermoso, J A]] | + | [[Category: Hermoso JA]] |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
BSR_VIBCH Amino-acid racemase able to utilize a broad range of substrates. Reversibly racemizes ten of the 19 natural chiral amino acids known, including both non-beta-branched aliphatic amino acids (Ala, Leu, Met, Ser, Cys, Gln and Asn) and positively charged amino acids (His, Lys and Arg). Among these substrates, is the most efficient with lysine and arginine. Is also able to catalyze the racemization of several amino acids that are not typically incorporated into proteins such as ornithine and norleucine. Is not active on negatively charged (Glu and Asp) or aromatic (Tyr, Trp and Phe) amino acids and displays minimal activity towards beta-branched aliphatic (Ile, Val and Thr) substrates (PubMed:24419381). Enables bacteria to produce and release extracellular non-canonical D-amino acids (NCDAAs) that regulate diverse cellular processes which may function as part of a cooperative strategy in vibrio communities to protect non-producing members from competing bacteria (PubMed:29446806, PubMed:29028003). D-amino acid production by BsrV provides a cue for V.cholerae to decrease peptidoglycan synthesis and to alter its cell wall via incorporation of NCDAAs into the muropeptides, in adaption to stationary phase conditions (PubMed:19762646, PubMed:29028003).[1] [2] [3] [4]
Publication Abstract from PubMed
Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical D-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be appreciated. Here, extensive crystallographic, mutational, biochemical and bioinformatic studies were used to define the molecular features of the racemase BsrV that enable this enzyme to accommodate more diverse substrates than the related PLP-dependent alanine racemases. Conserved residues were identified that distinguish BsrV and a newly defined family of broad-spectrum racemases from alanine racemases, and these residues were found to be key mediators of the multispecificity of BrsV. Finally, the structural analysis of an additional Bsr that was identified in the bioinformatic analysis confirmed that the distinguishing features of BrsV are conserved among Bsr family members.
Structural basis for the broad specificity of a new family of amino-acid racemases.,Espaillat A, Carrasco-Lopez C, Bernardo-Garcia N, Pietrosemoli N, Otero LH, Alvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):79-90. doi:, 10.1107/S1399004713024838. Epub 2013 Dec 24. PMID:24419381[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lam H, Oh DC, Cava F, Takacs CN, Clardy J, de Pedro MA, Waldor MK. D-amino acids govern stationary phase cell wall remodeling in bacteria. Science. 2009 Sep 18;325(5947):1552-5. doi: 10.1126/science.1178123. PMID:19762646 doi:http://dx.doi.org/10.1126/science.1178123
- ↑ Espaillat A, Carrasco-Lopez C, Bernardo-Garcia N, Pietrosemoli N, Otero LH, Alvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F. Structural basis for the broad specificity of a new family of amino-acid racemases. Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):79-90. doi:, 10.1107/S1399004713024838. Epub 2013 Dec 24. PMID:24419381 doi:http://dx.doi.org/10.1107/S1399004713024838
- ↑ Alvarez L, Aliashkevich A, de Pedro MA, Cava F. Bacterial secretion of D-arginine controls environmental microbial biodiversity. ISME J. 2018 Feb;12(2):438-450. doi: 10.1038/ismej.2017.176. Epub 2017 Oct 13. PMID:29028003 doi:http://dx.doi.org/10.1038/ismej.2017.176
- ↑ Cava F. Divergent functional roles of D-amino acids secreted by Vibrio cholerae. Int Microbiol. 2017 Sep;20(3):149-150. doi: 10.2436/20.1501.01.296. PMID:29446806 doi:http://dx.doi.org/10.2436/20.1501.01.296
- ↑ Espaillat A, Carrasco-Lopez C, Bernardo-Garcia N, Pietrosemoli N, Otero LH, Alvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F. Structural basis for the broad specificity of a new family of amino-acid racemases. Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):79-90. doi:, 10.1107/S1399004713024838. Epub 2013 Dec 24. PMID:24419381 doi:http://dx.doi.org/10.1107/S1399004713024838
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