PDBsum entry 3a8l

Lyase

PDB id: 3a8l

Contents

Protein chains

197 a.a. *

212 a.a. *

Metals

_FE

Waters ×635

* Residue conservation analysis

PDB id:

3a8l

Name:

Lyase

Title:

Crystal structure of photo-activation state of nitrile hydratase mutant s113a

Structure:

Nitrile hydratase subunit alpha. Chain: a. Synonym: nitrile hydratase alpha-subunit, nitrilase, nhase. Engineered: yes. Mutation: yes. Nitrile hydratase subunit beta. Chain: b. Synonym: nitrile hydratase beta-subunit, nitrilase, nhase. Engineered: yes

Source:

Rhodococcus erythropolis. Organism_taxid: 1833. Strain: n-771. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.63Å R-factor: 0.167 R-free: 0.191

Authors:

Y.Yamanaka,K.Hashimoto,A.Ohtaki,K.Noguchi,M.Yohda,M.Odaka

Key ref:

Y.Yamanaka et al. (2010). 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. PubMed id: 20221653

Date:

06-Oct-09 Release date: 14-Apr-10

Protein chain

P13448  (NHAA_RHOER) -  Nitrile hydratase subunit alpha from Rhodococcus erythropolis

Seq: 207 a.a.

Struc: 197 a.a.*

Protein chain

P13449  (NHAB_RHOER) -  Nitrile hydratase subunit beta from Rhodococcus erythropolis

Seq: 212 a.a.

Struc: 212 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.4.2.1.84 - nitrile hydratase.
• Reaction: an aliphatic primary amide = an aliphatic nitrile + H2O

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

J Biol Inorg Chem 15:655-665 (2010)

PubMed id: 20221653

Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase.

Y.Yamanaka, K.Hashimoto, A.Ohtaki, K.Noguchi, M.Yohda, M.Odaka.

ABSTRACT

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.