Crystal structure of O-ureidoserine racemase

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway.

Oda, K.Sakaguchi, T.Matoba, Y.

(2022) Proteins 90: 912-918

  • DOI: https://doi.org/10.1002/prot.26290
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The O-ureidoserine racemase (DcsC) is an enzyme found from the biosynthetic gene cluster of antitubercular agent d-cycloserine. Although DcsC is homologous to diaminopimelate epimerase (DapF) that catalyzes the interconversion between ll- and dl-diaminopimelic acid, it specifically catalyzes the interconversion between O-ureido-l-serine and its enantiomer. Here we determined the crystal structure of DcsC at a resolution of 2.12 Å, implicating that the catalytic mechanism of DcsC shares similarity with that of DapF. Comparing the structure of the active center of DcsC to that of DapF, Thr72, Thr198, and Tyr219 of DcsC are likely to be involved in the substrate specificity.

  • Organizational Affiliation

    Department of Virology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-ureido-serine racemase
A, B
295Streptomyces lavendulaeMutation(s): 0 
Gene Names: dcsCdapF
Find proteins for D2Z026 (Streptomyces lavendulae)
Explore D2Z026 
Go to UniProtKB:  D2Z026
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Z026
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.121α = 90
b = 96.051β = 92.13
c = 57.286γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description