1IRE

Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of cobalt-containing nitrile hydratase.

Miyanaga, A., Fushinobu, S., Ito, K., Wakagi, T.

(2001) Biochem.Biophys.Res.Commun. 288: 1169-1174

  • DOI: 10.1006/bbrc.2001.5897

  • PubMed Abstract: 

    • The crystal structure of cobalt-containing nitrile hydratase from Pseudonocardia thermophila JCM 3095 at 1.8 A resolution revealed the structure of the noncorrin cobalt at the catalytic center. Two cysteine residues (alphaCys(111) and alphaCys(113)) ...

    The crystal structure of cobalt-containing nitrile hydratase from Pseudonocardia thermophila JCM 3095 at 1.8 A resolution revealed the structure of the noncorrin cobalt at the catalytic center. Two cysteine residues (alphaCys(111) and alphaCys(113)) coordinated to the cobalt were posttranslationally modified to cysteine-sulfinic acid and to cysteine-sulfenic acid, respectively, like in iron-containing nitrile hydratase. A tryptophan residue (betaTrp(72)), which may be involved in substrate binding, replaced the tyrosine residue of iron-containing nitrile hydratase. The difference seems to be responsible for the preference for aromatic nitriles rather than aliphatic ones of cobalt-containing nitrile hydratase.

    Related Citations: 
    • Cloning and Sequencing of a Nitrile Hydratase Gene from Pseudonocardia thermophila JCM3095
      Yamaki, T.,Oikawa, T.,Ito, K.,Nakamura, T.
      (1997) J.FERMENT.BIOENG. 83: 474

    Organizational Affiliation: 

    Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrile Hydratase
A
204Pseudonocardia thermophilaMutation(s): 0 
EC: 4.2.1.84
Find proteins for Q7SID2 (Pseudonocardia thermophila)
Go to UniProtKB:  Q7SID2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nitrile Hydratase
B
228Pseudonocardia thermophilaMutation(s): 0 
EC: 4.2.1.84
Find proteins for Q7SID3 (Pseudonocardia thermophila)
Go to UniProtKB:  Q7SID3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO
Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.178 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.501α = 90.00
b = 65.501β = 90.00
c = 184.614γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance