6LUT

Crystal structure of Serine Racemase from Dictyostelium discoideum.

Summary for 6LUT

• Entry DOI: 10.2210/pdb6lut/pdb
• Descriptor: Probable serine racemase (2 entities in total)
• Functional Keywords: d-amino acid, racemase, plp, isomerase
• Biological source: Dictyostelium discoideum (Slime mold)
• Total number of polymer chains: 2
• Total formula weight: 72110.97

Authors

Goto, M.,Mizobuchi, T.,Yoshimura, T. (deposition date: 2020-01-31, release date: 2020-12-09, Last modification date: 2023-11-29)

Primary citation

Ito, T.,Matsuoka, M.,Goto, M.,Watanabe, S.,Mizobuchi, T.,Matsushita, K.,Nasu, R.,Hemmi, H.,Yoshimura, T.
Mechanism of eukaryotic serine racemase-catalyzed serine dehydration.
Biochim Biophys Acta Proteins Proteom, 1868:140460-140460, 2020

PubMed Abstract: Eukaryotic serine racemase (SR) is a pyridoxal 5'-phosphate enzyme belonging to the Fold-type II group, which catalyzes serine racemization and is responsible for the synthesis of D-Ser, a co-agonist of the N-methyl-d-aspartate receptor. In addition to racemization, SR catalyzes the dehydration of D- and L-Ser to pyruvate and ammonia. The bifuctionality of SR is thought to be important for D-Ser homeostasis. SR catalyzes the racemization of D- and L-Ser with almost the same efficiency. In contrast, the rate of L-Ser dehydration catalyzed by SR is much higher than that of D-Ser dehydration. This has caused the argument that SR does not catalyze the direct D-Ser dehydration and that D-Ser is first converted to L-Ser, then dehydrated. In this study, we investigated the substrate and solvent isotope effect of dehydration of D- and L-Ser catalyzed by SR from Dictyostelium discoideum (DdSR) and demonstrated that the enzyme catalyzes direct D-Ser dehydration. Kinetic studies of dehydration of four Thr isomers catalyzed by D. discoideum and mouse SRs suggest that SR discriminates the substrate configuration at C3 but not at C2. This is probably the reason for the difference in efficiency between L- and D-Ser dehydration catalyzed by SR.

PubMed: 32474107
DOI: 10.1016/j.bbapap.2020.140460

Experimental method

X-RAY DIFFRACTION (1.35 Å)