BRENDA - Enzyme Database

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

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
5.1.1.13
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
Scapharca broughtonii
Crystallization (Commentary)
EC Number
Crystallization
Organism
5.1.1.13
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
Scapharca broughtonii
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
5.1.1.13
malonate
-
Scapharca broughtonii
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
5.1.1.13
L-aspartate
Scapharca broughtonii
-
D-aspartate
-
-
r
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
5.1.1.13
Scapharca broughtonii
-
-
-
Purification (Commentary)
EC Number
Commentary
Organism
5.1.1.13
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
Scapharca broughtonii
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5.1.1.13
L-aspartate
-
746669
Scapharca broughtonii
D-aspartate
-
-
-
r
5.1.1.13
additional information
SbAspR catalyzes both racemization and dehydration. Residue Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR
746669
Scapharca broughtonii
?
-
-
-
-
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
5.1.1.13
pyridoxal 5'-phosphate
dependent on
Scapharca broughtonii
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
5.1.1.13
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
Scapharca broughtonii
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
5.1.1.13
pyridoxal 5'-phosphate
dependent on
Scapharca broughtonii
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
5.1.1.13
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
Scapharca broughtonii
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
5.1.1.13
malonate
-
Scapharca broughtonii
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
5.1.1.13
L-aspartate
Scapharca broughtonii
-
D-aspartate
-
-
r
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
5.1.1.13
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
Scapharca broughtonii
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5.1.1.13
L-aspartate
-
746669
Scapharca broughtonii
D-aspartate
-
-
-
r
5.1.1.13
additional information
SbAspR catalyzes both racemization and dehydration. Residue Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR
746669
Scapharca broughtonii
?
-
-
-
-
General Information
EC Number
General Information
Commentary
Organism
5.1.1.13
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
Scapharca broughtonii
5.1.1.13
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
Scapharca broughtonii
General Information (protein specific)
EC Number
General Information
Commentary
Organism
5.1.1.13
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
Scapharca broughtonii
5.1.1.13
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
Scapharca broughtonii