3anv

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{{STRUCTURE_3anv| PDB=3anv | SCENE= }}
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==Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)==
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===Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)===
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<StructureSection load='3anv' size='340' side='right' caption='[[3anv]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
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{{ABSTRACT_PUBMED_21676877}}
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== Structural highlights ==
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<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]. <br>
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</td></tr><tr><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><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3anu|3anu]]</td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
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<tr><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://www.rcsb.org/pdb/explore.do?structureId=3anv RCSB], [http://www.ebi.ac.uk/pdbsum/3anv PDBsum]</span></td></tr>
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<table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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 &gt;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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==About this Structure==
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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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[[3anv]] is a 1 chain structure with sequence from [http://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].
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==Reference==
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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<ref group="xtra">PMID:021676877</ref><references group="xtra"/><references/>
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</div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Chick]]
[[Category: D-serine ammonia-lyase]]
[[Category: D-serine ammonia-lyase]]
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[[Category: Gallus gallus]]
 
[[Category: Horiike, K.]]
[[Category: Horiike, K.]]
[[Category: Ishida, T.]]
[[Category: Ishida, T.]]

Revision as of 06:56, 14 May 2014

Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)

3anv, resolution 2.09Å

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