Crystal Structure of Modified Serine Racemase complexed with Serine

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe

Goto, M.Yamauchi, T.Kamiya, N.Miyahara, I.Yoshimura, T.Mihara, H.Kurihara, T.Hirotsu, K.Esaki, N.

(2009) J Biol Chem 284: 25944-25952

  • DOI: https://doi.org/10.1074/jbc.M109.010470
  • Primary Citation of Related Structures:  
    1WTC, 2ZR8

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein C320.14323Schizosaccharomyces pombeMutation(s): 0 
Find proteins for O59791 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O59791 
Go to UniProtKB:  O59791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59791
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.54α = 90
b = 72.88β = 101.73
c = 64.81γ = 90
Software Package:
Software NamePurpose
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2009-07-28 
  • Deposition Author(s): Goto, M.

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description