5YBW

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

Summary for 5YBW

• Entry DOI: 10.2210/pdb5ybw/pdb
• Descriptor: Aspartate racemase (2 entities in total)
• Functional Keywords: pyridoxal 5'-phosphate, aspartate racemase, scapharca broughtonii, serine racemase, isomerase
• Biological source: Scapharca broughtonii (Blood clam)
• Total number of polymer chains: 2
• Total formula weight: 72697.45

Authors

Mizobuchi, T.,Nonaka, R.,Yoshimura, M.,Abe, K.,Takahashi, S.,Kera, Y.,Goto, M. (deposition date: 2017-09-05, release date: 2017-12-20, Last modification date: 2023-11-22)

Primary citation

Mizobuchi, T.,Nonaka, R.,Yoshimura, M.,Abe, K.,Takahashi, S.,Kera, Y.,Goto, M.
Crystal structure of a pyridoxal 5'-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii
Acta Crystallogr F Struct Biol Commun, 73:651-656, 2017

PubMed Abstract: 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 Å 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 β-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.

PubMed: 29199985
DOI: 10.1107/S2053230X17015813

Experimental method

X-RAY DIFFRACTION (1.9 Å)