View source for 5ybw


==Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase==
<StructureSection load='5ybw' size='340' side='right'caption='[[5ybw]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ybw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anadara_broughtonii Anadara broughtonii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YBW FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></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=5ybw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybw OCA], [https://pdbe.org/5ybw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ybw RCSB], [https://www.ebi.ac.uk/pdbsum/5ybw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybw ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q2L695_ANABR Q2L695_ANABR] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Aspartate racemase (AspR) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that is responsible for D-aspartate biosynthesis in vivo. To the best of our knowledge, this is the first study to report an X-ray crystal structure of a PLP-dependent AspR, which was resolved at 1.90 A resolution. The AspR derived from the bivalve mollusc Scapharca broughtonii (SbAspR) is a type II PLP-dependent enzyme that is similar to serine racemase (SR) in that SbAspR catalyzes both racemization and dehydration. Structural comparison of SbAspR and SR shows a similar arrangement of the active-site residues and nucleotide-binding site, but a different orientation of the metal-binding site. Superposition of the structures of SbAspR and of rat SR bound to the inhibitor malonate reveals that Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR. It is hypothesized that the aromatic proline interaction between the domains, which favours the closed form of SbAspR, influences the arrangement of Arg140 at the active site.

Crystal structure of a pyridoxal 5'-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii.,Mizobuchi T, Nonaka R, Yoshimura M, Abe K, Takahashi S, Kera Y, Goto M Acta Crystallogr F Struct Biol Commun. 2017 Dec 1;73(Pt 12):651-656. doi:, 10.1107/S2053230X17015813. Epub 2017 Nov 6. PMID:29199985<ref>PMID:29199985</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ybw" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Anadara broughtonii]]
[[Category: Large Structures]]
[[Category: Abe K]]
[[Category: Goto M]]
[[Category: Kera Y]]
[[Category: Mizobuchi T]]
[[Category: Nonaka R]]
[[Category: Takahashi S]]
[[Category: Yoshimura M]]