3anv: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<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>
<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" 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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.09&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3anu|3anu]]</div></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'>[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=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'>[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>
</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 &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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3anv" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: D-serine ammonia-lyase]]
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
[[Category: Large Structures]]
[[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]]
[[Category: Lyase]]
[[Category: Plp binding]]
[[Category: Plp-dependent fold-type iii enzyme]]
[[Category: Zinc binding]]

Latest revision as of 11:40, 7 February 2024

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)

Structural highlights

3anv is a 1 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.09Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A8V1ABE9_CHICK

3anv, resolution 2.09Å

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
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