Literature summary for 5.1.1.18 extracted from

Goto, M.; Yamauchi, T.; Kamiya, N.; Miyahara, I.; Yoshimura, T.; Mihara, H.; Kurihara, T.; Hirotsu, K.; Esaki, N.
Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe (2009), J. Biol. Chem., 284, 25944-25952.

Activating Compound

Activating Compound	Comment	Organism	Structure
ATP	as MgATP2-, the ATP binding site is located at the domain and the subunit interface	Schizosaccharomyces pombe

Crystallization (Commentary)

Crystallization (Comment)	Organism
free wild-type enzyme, wild-type enzyme in complex with the ATP analogue AMP-PCP, and the modified enzyme in complex with serine, vapor diffusion method at 20°C, 0.003 ml of protein solution with 2.2 mg/ml protein and 10 mM Tris-HCl buffer, pH 8.0, are mixed with an equal volume of reservoir solution containing 28% w/v PEG 4000, 200 mM sodium acetate, and 100 mM Tris-HCl, pH 8.5, and equilibrated against 450 ml of the reservoir solution, for the ligand complexed enzyme, 10 mM AMP-PCP and 0.2 M MgCl2 are added, X-ray diffraction structure determination and analysis at at 1.7 A, 1.9 A, and 2.2 A resolution, respectively	Schizosaccharomyces pombe

Crystallization (Comment)

Organism

free wild-type enzyme, wild-type enzyme in complex with the ATP analogue AMP-PCP, and the modified enzyme in complex with serine, vapor diffusion method at 20°C, 0.003 ml of protein solution with 2.2 mg/ml protein and 10 mM Tris-HCl buffer, pH 8.0, are mixed with an equal volume of reservoir solution containing 28% w/v PEG 4000, 200 mM sodium acetate, and 100 mM Tris-HCl, pH 8.5, and equilibrated against 450 ml of the reservoir solution, for the ligand complexed enzyme, 10 mM AMP-PCP and 0.2 M MgCl2 are added, X-ray diffraction structure determination and analysis at at 1.7 A, 1.9 A, and 2.2 A resolution, respectively

Schizosaccharomyces pombe

Protein Variants

Protein Variants	Comment	Organism
additional information	construction of a modified enzyme, which has a unique lysino-D-alanyl residue at the active site, and also exhibits catalytic activities. The substrate serine is actually trapped in the active site of the modified enzyme, suggesting that the lysino-D-alanyl residue acts as a catalytic base in the same manner as inherent Lys57 of the wild-type enzyme	Schizosaccharomyces pombe
S82A	site-directed mutagenesis	Schizosaccharomyces pombe

Inhibitors

Inhibitors	Comment	Organism	Structure
AMP-PCP	Mg-AMP-PCP is bound to the groove formed at the intersection between the domain interface and the subunit interface, structure and binding mode, overview. The binding of Mg-AMP-PCP to the enzyme in the open form does not induce a subunit conformational change, but, interestingly, changes the relative orientation between the two subunits	Schizosaccharomyces pombe

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	as MgATP2-, activates	Schizosaccharomyces pombe

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
L-serine	Schizosaccharomyces pombe	-	D-serine	-	r

Organism

Organism	UniProt	Comment	Textmining
Schizosaccharomyces pombe	O59791	-	-

Reaction

Reaction	Comment	Organism	Reaction ID
L-serine = D-serine	substrate recognition mechanism and catalytic mechanisms of both reactions, the racemization and the dehydration of serine, residues Lys57 and Ser82 located on the protein and solvent sides, respectively, with respect to the cofactor plane, are acid-base catalysts that shuttle protons to the substrate. Racemization mechanism via carbanion intermediate, alpha-aminoacrylate intermediate, and pyridoxal 5'-phosphate-lysine-D-alanine Schiff base	Schizosaccharomyces pombe	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
L-serine	-	Schizosaccharomyces pombe	D-serine	-	r
L-serine	on binding of the substrate, the small domain rotates toward the large domain to close the active site, substrate binding structure, Lys57 is the catalytic residue of the wild-type enzyme, overview	Schizosaccharomyces pombe	D-serine	-	r
additional information	the enzyme also catalyzes the dehydration of D- and L-serine resulting in pyruvate	Schizosaccharomyces pombe	?	-	?

Subunits

Subunits	Comment	Organism
More	enzyme monomer and dimer structures, three-dimensional structure, overview. Structural model of external aldimine of the wild-type enzyme	Schizosaccharomyces pombe

Cofactor

Cofactor	Comment	Organism	Structure
pyridoxal 5'-phosphate	dependent on, binding structure, overview	Schizosaccharomyces pombe