Crystal Structure of L-N-carbamoylase from Geobacillus stearothermophilus CECT43

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Mutational and structural analysis of L-N-carbamoylase reveals new insights into a peptidase m20/m25/m40 family member.

Martinez-Rodriguez, S.Garcia-Pino, A.Las Heras-Vazquez, F.J.Clemente-Jimenez, J.M.Rodriguez-Vico, F.Garcia-Ruiz, J.M.Loris, R.Gavira, J.A.

(2012) J Bacteriol 194: 5759-5768

  • DOI: https://doi.org/10.1128/JB.01056-12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    N-Carbamoyl-L-amino acid amidohydrolases (L-carbamoylases) are important industrial enzymes used in kinetic resolution of racemic mixtures of N-carbamoyl-amino acids due to their strict enantiospecificity. In this work, we report the first L-carbamoylase structure belonging to Geobacillus stearothermophilus CECT43 (BsLcar), at a resolution of 2.7 Å. Structural analysis of BsLcar and several members of the peptidase M20/M25/M40 family confirmed the expected conserved residues at the active site in this family, and site-directed mutagenesis revealed their relevance to substrate binding. We also found an unexpectedly conserved arginine residue (Arg(234) in BsLcar), proven to be critical for dimerization of the enzyme. The mutation of this sole residue resulted in a total loss of activity and prevented the formation of the dimer in BsLcar. Comparative studies revealed that the dimerization domain of the peptidase M20/M25/M40 family is a "small-molecule binding domain," allowing further evolutionary considerations for this enzyme family.

  • Organizational Affiliation

    Departamento de Química Física, Bioquímica y Química Inorgánica, Universidad de Almería, Almería, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-carbamoyl-L-amino acid hydrolase
A, B
408Geobacillus stearothermophilusMutation(s): 0 
Gene Names: amaB
Find proteins for Q53389 (Geobacillus stearothermophilus)
Explore Q53389 
Go to UniProtKB:  Q53389
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53389
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.208α = 90
b = 211.683β = 90
c = 43.091γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-31
    Changes: Database references
  • Version 1.3: 2012-11-14
    Changes: Database references
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description