3A8L image
Deposition Date 2009-10-06
Release Date 2010-04-14
Last Version Date 2024-10-23
Entry Detail
PDB ID:
3A8L
Keywords:
Title:
Crystal structure of photo-activation state of Nitrile Hydratase mutant S113A
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.63 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Nitrile hydratase subunit alpha
Gene (Uniprot):nthA
Mutations:S113A
Chain IDs:A
Chain Length:207
Number of Molecules:1
Biological Source:Rhodococcus erythropolis
Polymer Type:polypeptide(L)
Molecule:Nitrile hydratase subunit beta
Gene (Uniprot):nthB
Chain IDs:B
Chain Length:212
Number of Molecules:1
Biological Source:Rhodococcus erythropolis
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CSD A CYS 3-SULFINOALANINE
CSO A CYS S-HYDROXYCYSTEINE
Ligand Molecules
Primary Citation
Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase
J.Biol.Inorg.Chem. 15 655 665 (2010)
PMID: 20221653 DOI: 10.1007/s00775-010-0632-3

Abstact

Nitrile hydratases (NHase), which catalyze the hydration of nitriles to amides, have an unusual Fe(3+) or Co(3+) center with two modified Cys ligands: cysteine sulfininate (Cys-SO(2) (-)) and either cysteine sulfenic acid or cysteine sulfenate [Cys-SO(H)]. Two catalytic mechanisms have been proposed. One is that the sulfenyl oxygen activates a water molecule, enabling nucleophilic attack on the nitrile carbon. The other is that the Ser ligand ionizes the strictly conserved Tyr, activating a water molecule. Here, we characterized mutants of Fe-type NHase from Rhodococcus erythropolis N771, replacing the Ser and Tyr residues, alphaS113A and betaY72F. The alphaS113A mutation partially affected catalytic activity and did not change the pH profiles of the kinetic parameters. UV-vis absorption spectra indicated that the electronic state of the Fe center was altered by the alphaS113A mutation, but the changes could be prevented by a competitive inhibitor, n-butyric acid. The overall structure of the alphaS113A mutant was similar to that of the wild type, but significant changes were observed around the catalytic cavity. Like the UV-vis spectra, the changes were compensated by the substrate or product. The Ser ligand is important for the structure around the catalytic cavity, but is not essential for catalysis. The betaY72F mutant exhibited no activity. The structure of the betaY72F mutant was highly conserved but was found to be the inactivated state, with alphaCys114-SO(H) oxidized to Cys-SO(2) (-), suggesting that betaTyr72 affected the electronic state of the Fe center. The catalytic mechanism is discussed on the basis of the results obtained.

Legend

Protein

Chemical

Disease

Primary Citation of related structures