3N5F

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1128/JB.01056-12
  • Structures With Same Primary Citation

  • 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-carbamoy ...

    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.


    Related Citations: 
    • Crystallization and preliminary crystallographic studies of the recombinant L-N-carbamoylase from Geobacillus stearothermophilus CECT43.
      Martinez-Rodriguez, S., Garcia-Pino, A., Las Heras-Vazquez, F.J., Clemente-Jimenez, J.M., Rodriguez-Vico, F., Loris, R., Garcia-Ruiz, J.M., Gavira, J.A.
      (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 1135

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-carbamoyl-L-amino acid hydrolase
A, B
408Geobacillus stearothermophilusMutation(s): 0 
Gene Names: amaB
EC: 3.5.1.87
Find proteins for Q53389 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q53389
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download CCD File 
B
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
IPA
Query on IPA

Download CCD File 
A, B
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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