This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3awn

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:36, 1 November 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3awn.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of D-serine dehydratase from chicken kidney (EDTA treated)==
-
The line below this paragraph, containing "STRUCTURE_3awn", creates the "Structure Box" on the page.
+
<StructureSection load='3awn' size='340' side='right'caption='[[3awn]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3awn]] 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=3AWN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AWN FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-
{{STRUCTURE_3awn| PDB=3awn | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3awn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3awn OCA], [https://pdbe.org/3awn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3awn RCSB], [https://www.ebi.ac.uk/pdbsum/3awn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3awn ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/A0A8V1ABE9_CHICK A0A8V1ABE9_CHICK]
 +
<div style="background-color:#fffaf0;">
 +
== 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 &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 D-serine dehydratase from chicken kidney (EDTA treated)===
+
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>
-
==About this Structure==
+
</div>
-
[[3awn]] 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=3AWN OCA].
+
<div class="pdbe-citations 3awn" style="background-color:#fffaf0;"></div>
-
[[Category: D-serine ammonia-lyase]]
+
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
-
[[Category: Horiike, K.]]
+
[[Category: Large Structures]]
-
[[Category: Ishida, T.]]
+
[[Category: Horiike K]]
-
[[Category: Senda, M.]]
+
[[Category: Ishida T]]
-
[[Category: Senda, T.]]
+
[[Category: Senda M]]
-
[[Category: Tanaka, H.]]
+
[[Category: Senda T]]
-
[[Category: Venugopalan, N.]]
+
[[Category: Tanaka H]]
-
[[Category: Yamamoto, A.]]
+
[[Category: Venugopalan N]]
-
[[Category: D-serine dehydratase]]
+
[[Category: Yamamoto A]]
-
[[Category: Lyase]]
+
-
[[Category: Plp binding]]
+
-
[[Category: Plp-dependent fold-type iii enzyme]]
+
-
[[Category: Zinc binding]]
+

Current revision

Crystal structure of D-serine dehydratase from chicken kidney (EDTA treated)

PDB ID 3awn

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3awn"
Personal tools