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| ==Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)== | | ==Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)== |
| <StructureSection load='3anv' size='340' side='right' caption='[[3anv]], [[Resolution|resolution]] 2.09Å' scene=''> | | <StructureSection load='3anv' size='340' side='right'caption='[[3anv]], [[Resolution|resolution]] 2.09Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[3anv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ANV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ANV FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3anv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ANV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ANV FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2RA:3-AMINO-D-ALANINE'>2RA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.09Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3anu|3anu]]</td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2RA:3-AMINO-D-ALANINE'>2RA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [http://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=3anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3anv OCA], [https://pdbe.org/3anv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3anv RCSB], [https://www.ebi.ac.uk/pdbsum/3anv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3anv 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=3anv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3anv OCA], [http://pdbe.org/3anv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3anv RCSB], [http://www.ebi.ac.uk/pdbsum/3anv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3anv ProSAT]</span></td></tr> | |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
| | == Function == |
| == Publication Abstract from PubMed == | | [https://www.uniprot.org/uniprot/A0A8V1ABE9_CHICK A0A8V1ABE9_CHICK] |
| D-serine is a physiological co-agonist of the N-methyl-D-aspartate receptor. It regulates excitatory neurotransmission, which is important for higher brain functions in vertebrates. In mammalian brains, D-amino acid oxidase degrades D-serine. However, we have found recently that in chicken brains the oxidase is not expressed and instead a D-serine dehydratase degrades D-serine. The primary structure of the enzyme shows significant similarities to those of metal-activated D-threonine aldolases, which are fold-type III pyridoxal 5'-phosphate (PLP)-dependent enzymes, suggesting that it is a novel class of D-serine dehydratase. In the present study, we characterized the chicken enzyme biochemically and also by x-ray crystallography. The enzyme activity on D-serine decreased 20-fold by EDTA treatment and recovered nearly completely by the addition of Zn(2+). None of the reaction products that would be expected from side reactions of the PLP-D-serine Schiff base were detected during the >6000 catalytic cycles of dehydration, indicating high reaction specificity. We have determined the first crystal structure of the D-serine dehydratase at 1.9 A resolution. In the active site pocket, a zinc ion that coordinates His(347) and Cys(349) is located near the PLP-Lys(45) Schiff base. A theoretical model of the enzyme-D-serine complex suggested that the hydroxyl group of D-serine directly coordinates the zinc ion, and that the epsilon-NH(2) group of Lys(45) is a short distance from the substrate Calpha atom. The alpha-proton abstraction from D-serine by Lys(45) and the elimination of the hydroxyl group seem to occur with the assistance of the zinc ion, resulting in the strict reaction specificity.
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| Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney.,Tanaka H, Senda M, Venugopalan N, Yamamoto A, Senda T, Ishida T, Horiike K J Biol Chem. 2011 Aug 5;286(31):27548-58. Epub 2011 Jun 15. PMID:21676877<ref>PMID:21676877</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 3anv" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Chick]] | | [[Category: Gallus gallus]] |
| [[Category: D-serine ammonia-lyase]] | | [[Category: Large Structures]] |
| [[Category: Horiike, K]] | | [[Category: Horiike K]] |
| [[Category: Ishida, T]] | | [[Category: Ishida T]] |
| [[Category: Senda, M]] | | [[Category: Senda M]] |
| [[Category: Senda, T]] | | [[Category: Senda T]] |
| [[Category: Tanaka, H]] | | [[Category: Tanaka H]] |
| [[Category: Venugopalan, N]] | | [[Category: Venugopalan N]] |
| [[Category: Yamamoto, A]] | | [[Category: Yamamoto A]] |
| [[Category: D-serine dehydratase]]
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| [[Category: Lyase]]
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| [[Category: Plp binding]]
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| [[Category: Plp-dependent fold-type iii enzyme]]
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| [[Category: Zinc binding]]
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