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 

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

  • 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.,Sect.D 55: 694


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE
A, B, C, D
304Rhizobium radiobacterMutation(s): 0 
EC: 3.5.1.77
Find proteins for Q44185 (Rhizobium radiobacter)
Go to UniProtKB:  Q44185
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XE
Query on XE

Download SDF File 
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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.230α = 90.00
b = 67.530β = 96.12
c = 137.480γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
MOSFLMdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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