Literature summary for 5.1.1.13 extracted from

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 (2017), Acta Crystallogr. Sect. F, 73, 651-656 .

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)	Anadara broughtonii

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, mixing of 0.006 ml of 2.5 mg/ml protein in 10 mM Tris-HCl, 20 mM pyridoxal 5'-phosphate, 1 mM 2-mercaptoethanol, pH 8.8, with 0.003 ml of reservoir solution containing 27% w/v PEG 4000, 50 mM sodium acetate, pH 5.0, 200 mM ammonium acetate, and 15% v/v glycerol, and equilibration against 0.1 ml of reservoir solution, 14°C, X-ray diffraction structure determination and analysis at 1.90 A resolution	Anadara broughtonii

Crystallization (Comment)

Organism

purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, mixing of 0.006 ml of 2.5 mg/ml protein in 10 mM Tris-HCl, 20 mM pyridoxal 5'-phosphate, 1 mM 2-mercaptoethanol, pH 8.8, with 0.003 ml of reservoir solution containing 27% w/v PEG 4000, 50 mM sodium acetate, pH 5.0, 200 mM ammonium acetate, and 15% v/v glycerol, and equilibration against 0.1 ml of reservoir solution, 14°C, X-ray diffraction structure determination and analysis at 1.90 A resolution

Anadara broughtonii

Inhibitors

Inhibitors	Comment	Organism	Structure
malonate	-	Anadara broughtonii

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
L-aspartate	Anadara broughtonii	-	D-aspartate	-	r

Organism

Organism	UniProt	Comment	Textmining
Anadara broughtonii	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography	Anadara broughtonii

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
L-aspartate	-	Anadara broughtonii	D-aspartate	-	r
additional information	SbAspR catalyzes both racemization and dehydration. Residue Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR	Anadara broughtonii	?	-	?

Synonyms

Synonyms	Comment	Organism
AspR	-	Anadara broughtonii
SbAspR	-	Anadara broughtonii

Cofactor

Cofactor	Comment	Organism	Structure
pyridoxal 5'-phosphate	dependent on	Anadara broughtonii

General Information

General Information	Comment	Organism
additional information	residue Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR. The aromatic proline interaction between the domains, which favours the closed form of SbAspR, might influence the arrangement of Arg140 at the active site, active site structure of SbAspR, overview	Anadara broughtonii
physiological function	the enzyme is responsible for D-aspartate biosynthesis in vivo. Enzyme SbAspR is a type II PLP-dependent enzyme. D-Aspartate is one of the most abundant free D-amino acids present in the nervous and reproductive systems and plays important physiological roles, including regulating developmental processes, hormone secretion and steroidogenesis	Anadara broughtonii