2ZR8 image
Entry Detail
PDB ID:
2ZR8
Keywords:
Title:
Crystal Structure of Modified Serine Racemase complexed with Serine
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2008-08-25
Release Date:
2009-07-28
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Uncharacterized protein C320.14
Chain IDs:A
Chain Length:323
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe
Primary Citation
Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe
J.Biol.Chem. 284 25944 25952 (2009)
PMID: 19640845 DOI: 10.1074/jbc.M109.010470

Abstact

D-serine is an endogenous coagonist for the N-methyl-D-aspartate receptor and is involved in excitatory neurotransmission in the brain. Mammalian pyridoxal 5'-phosphate-dependent serine racemase, which is localized in the mammalian brain, catalyzes the racemization of L-serine to yield D-serine and vice versa. The enzyme also catalyzes the dehydration of D- and L-serine. Both reactions are enhanced by Mg.ATP in vivo. We have determined the structures of the following three forms of the mammalian enzyme homolog from Schizosaccharomyces pombe: the wild-type enzyme, the wild-type enzyme in the complex with an ATP analog, and the modified enzyme in the complex with serine at 1.7, 1.9, and 2.2 A resolution, respectively. On binding of the substrate, the small domain rotates toward the large domain to close the active site. The ATP binding site was identified at the domain and the subunit interface. Computer graphics models of the wild-type enzyme complexed with L-serine and D-serine provided an insight into the catalytic mechanisms of both reactions. Lys-57 and Ser-82 located on the protein and solvent sides, respectively, with respect to the cofactor plane, are acid-base catalysts that shuttle protons to the substrate. The modified enzyme, which has a unique "lysino-D-alanyl" residue at the active site, also exhibits catalytic activities. The crystal-soaking experiment showed that the substrate serine was 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 Lys-57 of the wild-type enzyme.

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