5ybw

Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase

spinqualitylabelsall models 5ybw, resolution 1.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5ybw is a 2 chain structure with sequence from Anadara broughtonii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.9Å Ligands: LLP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q2L695_ANABR 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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