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3anv

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Revision as of 12:24, 29 July 2020

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.
Ligands:	, , ,
Related:	3anu
Activity:	D-serine ammonia-lyase, with EC number 4.3.1.18
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tanaka H, Senda M, Venugopalan N, Yamamoto A, Senda T, Ishida T, Horiike K. Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney. J Biol Chem. 2011 Aug 5;286(31):27548-58. Epub 2011 Jun 15. PMID:21676877 doi:10.1074/jbc.M110.201160

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3anv"

@@ Line 1: / Line 1: @@
 ==Crystal structure of D-serine dehydratase from chicken kidney (2,3-DAP complex)==
-<StructureSection load='3anv' size='340' side='right' caption='[[3anv]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
+<StructureSection load='3anv' size='340' side='right'caption='[[3anv]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[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]. 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 [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]. For a <b>guided tour on the structure components</b> use [http://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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3anu|3anu]]</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'>[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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/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>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 24: @@
 [[Category: D-serine ammonia-lyase]]
 [[Category: Gallus gallus]]
+[[Category: Large Structures]]
 [[Category: Horiike, K]]
 [[Category: Ishida, T]]

3anv

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Revision as of 12:24, 29 July 2020

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

Structural highlights

Publication Abstract from PubMed

References

Contents

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