1IRE

Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila

• PDB DOI: https://doi.org/10.2210/pdb1IRE/pdb

• Classification: LYASE
• Organism(s): Pseudonocardia thermophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-10-01 Released: 2002-10-01 
• Deposition Author(s): Miyanaga, A., Fushinobu, S., Ito, K., Wakagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.191 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Crystal structure of cobalt-containing nitrile hydratase.

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

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

• PubMed: 11700034 
• DOI: https://doi.org/10.1006/bbrc.2001.5897
• Primary Citation of Related Structures:  
  1IRE


• 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)) 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 49.45 kDa 
• Atom Count: 3,793 
• Modelled Residue Count: 431 
• Deposited Residue Count: 432 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile Hydratase	A	204	Pseudonocardia thermophila	Mutation(s): 0  EC: 4.2.1.84
UniProt
Find proteins for Q7SID2 (Pseudonocardia thermophila) Explore Q7SID2  Go to UniProtKB:  Q7SID2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile Hydratase	B	228	Pseudonocardia thermophila	Mutation(s): 0  EC: 4.2.1.84
UniProt
Find proteins for Q7SID3 (Pseudonocardia thermophila) Explore Q7SID3  Go to UniProtKB:  Q7SID3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.191 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.501	α = 90
b = 65.501	β = 90
c = 184.614	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-01 
Deposition Author(s): Miyanaga, A., Fushinobu, S., Ito, K., Wakagi, T.

Revision History  

• Version 1.0: 2002-10-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection