1FO6

CRYSTAL STRUCTURE ANALYSIS OF N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter reveals a homotetramer and insight into a catalytic cleft.

Wang, W.C.Hsu, W.H.Chien, F.T.Chen, C.Y.

(2001) J Mol Biol 306: 251-261

  • DOI: 10.1006/jmbi.2000.4380
  • Primary Citation of Related Structures:  
    1FO6

  • PubMed Abstract: 
  • The N-carbamoyl-D-amino-acid amidohydrolase (D-NCAase) is used on an industrial scale for the production of D-amino acids. The crystal structure of D-NCAase was solved by multiple isomorphous replacement with anomalous scattering using xenon and gold ...

    The N-carbamoyl-D-amino-acid amidohydrolase (D-NCAase) is used on an industrial scale for the production of D-amino acids. The crystal structure of D-NCAase was solved by multiple isomorphous replacement with anomalous scattering using xenon and gold derivatives, and refined to 1.95 A resolution, to an R-factor of 18.6 %. The crystal structure shows a four-layer alpha/beta fold with two six-stranded beta sheets packed on either side by two alpha helices. One exterior layer faces the solvent, whereas the other one is buried and involved in the tight intersubunit contacts. A long C-terminal fragment extends from a monomer to a site near a dyad axis, and associates with another monomer to form a small and hydrophobic cavity, where a xenon atom can bind. Site-directed mutagenesis of His129, His144 and His215 revealed strict geometric requirements of these conserved residues to maintain a stable conformation of a putative catalytic cleft. A region located within this cleft involving Cys172, Glu47, and Lys127 is proposed for D-NCAase catalysis and is similar to the Cys-Asp-Lys site of N-carbamoylsarcosine amidohydrolase. The homologous active-site framework of these enzymes with distinct structures suggests convergent evolution of a common catalytic mechanism.


    Related Citations: 
    • Expression, crystallization and preliminary X-ray diffraction studies of N-carbamyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter
      Hsu, W.-H., Chien, F.-T., Hsu, C.L., Wang, T.C., Yuan, H.S., Wang, W.-C.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 694

    Organizational Affiliation

    Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan. lswwc@dragon.nchu.edu.tw



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASEABCD304Agrobacterium tumefaciensMutation(s): 0 
EC: 3.4.22.12 (PDB Primary Data), 3.5.1.77 (UniProt)
Find proteins for Q44185 (Rhizobium radiobacter)
Explore Q44185 
Go to UniProtKB:  Q44185
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XE
Query on XE

Download CCD File 
B, C
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.23α = 90
b = 67.53β = 96.12
c = 137.48γ = 90
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance