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| | <StructureSection load='3r0z' size='340' side='right'caption='[[3r0z]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='3r0z' size='340' side='right'caption='[[3r0z]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R0Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R0Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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]] 2.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r0x|3r0x]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dsdA, STM3802 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18] </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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [https://pdbe.org/3r0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [https://www.ebi.ac.uk/pdbsum/3r0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r0z 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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [https://pdbe.org/3r0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [https://www.ebi.ac.uk/pdbsum/3r0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r0z ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/SDHD_SALTY SDHD_SALTY] |
| - | Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-Serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the co-factor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modeling suggests that Thr 166 may be involved in abstraction of proton from the Calpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses alpha, beta elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.
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| - | | + | |
| - | Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis.,Bharath SR, Bisht S, Savithri HS, Murthy MR FEBS J. 2011 Jun 10. doi: 10.1111/j.1742-4658.2011.08210.x. PMID:21668644<ref>PMID:21668644</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3r0z" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Deaminase 3D structures|Deaminase 3D structures]] | | *[[Deaminase 3D structures|Deaminase 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus typhimurium loeffler 1892]] | |
| - | [[Category: D-serine ammonia-lyase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bharath, S R]] | + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium]] |
| - | [[Category: Murthy, M R.N]]
| + | [[Category: Bharath SR]] |
| - | [[Category: Savithri, H S]] | + | [[Category: Murthy MRN]] |
| - | [[Category: Shveta, B]] | + | [[Category: Savithri HS]] |
| - | [[Category: Alpha]] | + | [[Category: Shveta B]] |
| - | [[Category: Beta elimination of d-serine]] | + | |
| - | [[Category: Foldtype 2 family of plp-dependent enzyme]]
| + | |
| - | [[Category: Lyase]]
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