D-Fining DarR, a LysR-Type Transcriptional Regulator That Responds to D-Aspartate

ABSTRACT Work by Jones et al. (R. M. Jones, Jr., D. L. Popham, A. L. Schmidt, E. L. Neidle, and E. V. Stabb, J Bacteriol 200:e00773-17, 2018, https://doi.org/10.1128/JB.00773-17) describes a d-aspartate-sensing system in proteobacteria. d-Amino acids are critical components of peptidoglycan and other structures. The new study identifies the LysR-type transcriptional regulator DarR, which activates the aspartate racemase RacD. The overexpression of RacD enables it to synthesize d-glutamate and restore normal peptidoglycan in a Vibrio fischeri murI mutant. This study contributes to the understanding of emerging roles for d-amino acids and how they are synthesized under distinct conditions.

Crystal structure of a pyridoxal 5′-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii

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.