Activating Compound | Comment | Organism | Structure |
---|---|---|---|
ATP | as MgATP2-, the ATP binding site is located at the domain and the subunit interface | 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 | 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 | 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 | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | as MgATP2-, activates | Schizosaccharomyces pombe |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
L-serine | Schizosaccharomyces pombe | - |
D-serine | - |
r |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Schizosaccharomyces pombe | O59791 | - |
- |
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 |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
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 | 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 | Comment | Organism | Structure |
---|---|---|---|
pyridoxal 5'-phosphate | dependent on, binding structure, overview | Schizosaccharomyces pombe |