› 3x26

X-ray diffraction
1.34Å resolution

Crystal structure of Nitrile Hydratase mutant bR56K complexed with Trimethylacetonitrile, photo-activated for 5 min

Released:
DOI: 10.2210/pdb3x26/pdb
PDB entry 3x26 coloured by chain, front view.
PDB entry 3x26 coloured by chain, side view.
PDB entry 3x26 coloured by chain, top view.
Source organism: Rhodococcus erythropolis
Primary publication:
Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile.
Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M
Angew Chem Int Ed Engl 54 10763-7 (2015)
PMID: 26333053

Function and Biology Details

Reaction catalysed: 
An aliphatic amide = a nitrile + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146592 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Nitrile hydratase subunit alpha Chain: A
Molecule details ›
Chain: A
Length: 207 amino acids
Theoretical weight: 23.07 KDa
Source organism: Rhodococcus erythropolis
Expression system: Escherichia coli
UniProt:
  • Canonical: P13448 (Residues: 1-207; Coverage: 100%)
Gene name: nthA
Sequence domains: Nitrile hydratase, alpha chain
Structure domains: Nitrile hydratase alpha /Thiocyanate hydrolase gamma
Nitrile hydratase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 212 amino acids
Theoretical weight: 23.49 KDa
Source organism: Rhodococcus erythropolis
Expression system: Escherichia coli
UniProt:
  • Canonical: P13449 (Residues: 1-212; Coverage: 100%)
Gene names: nha2, nthB
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand FE 1 x FE
Ligand MG 2 x MG
Ligand CL 4 x CL
Ligand TAN 1 x TAN
2 modified residues:
Ligand CSD 1 x CSD
Ligand CSO 1 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: C2
Unit cell:
a: 113.861Å b: 59.953Å c: 81.594Å
α: 90° β: 125.08° γ: 90°
R-values:
R R work R free
0.174 0.173 0.194
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Advances in cloning, structural and bioremediation aspects of nitrile hydratases.
Supreetha et al. (2019)
1 more