PDBsum entry: 1ahj

Lyase

PDB id: 1ahj

Contents

Protein chains

198 a.a. *

212 a.a. *

Metals

_FE ×4

* Residue conservation analysis

PDB id:

1ahj

Name:

Lyase

Title:

Nitrile hydratase

Structure:

Nitrile hydratase (subunit alpha). Chain: a, c, e, g. Nitrile hydratase (subunit beta). Chain: b, d, f, h. Ec: 4.2.1.84

Source:

Rhodococcus sp. R312. Organism_taxid: 76275. Organism_taxid: 76275

Biol. unit:

Hetero-Dimer (from PDB file)

Resolution:

2.65Å R-factor: 0.264 R-free: 0.289

Authors:

W.Huang,G.Schneider,Y.Lindqvist

Key ref:

W.Huang et al. (1997). Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold. Structure, 5, 691-699. PubMed id: 9195885 DOI: 10.1016/S0969-2126(97)00223-2

Date:

05-Apr-97 Release date: 08-Apr-98

Protein chains

P13448  (NHAA_RHOER) -  Nitrile hydratase subunit alpha

Seq: 207 a.a.

Struc: 198 a.a.*

Protein chains

P13449  (NHAB_RHOER) -  Nitrile hydratase subunit beta

Seq: 212 a.a.

Struc: 212 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.4.2.1.84 - Nitrile hydratase.
• Reaction: An aliphatic amide = a nitrile + H₂O

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

 Gene Ontology (GO) functional annotation 

• Cellular component: plastid (1 term)
• Biological process: nitrogen compound metabolic process (2 terms)
• Biochemical function: catalytic activity (6 terms)

Added reference

DOI no: 10.1016/S0969-2126(97)00223-2

Structure 5:691-699 (1997)

PubMed id: 9195885

Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold.

W.Huang, J.Jia, J.Cummings, M.Nelson, G.Schneider, Y.Lindqvist.

ABSTRACT

BACKGROUND: Nitrile hydratases are unusual metalloenzymes that catalyze the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alphabeta unit. We have determined the crystal structure of photoactivated iron-containing nitrile hydratase from Rhodococcus sp. R312 to 2.65 A resolution as a first step in the elucidation of its catalytic mechanism. RESULTS: The alpha subunit consists of a long N-terminal arm and a C-terminal domain that forms a novel fold. This fold can be described as a four layered structure, alpha-beta-beta-alpha, with unusual connectivities between the beta strands. The beta subunit also contains a long N-terminal extension, a helical domain, and a C-terminal domain that folds into a beta roll. The two subunits form a tight heterodimer that is the functional unit of the enzyme. The active site is located in a cavity at the subunit-subunit interface. The iron centre is formed by residues from the alpha subunit only-three cysteine thiolates and two mainchain amide nitrogen atoms are ligands. CONCLUSIONS: Nitrile hydratases contain a novel iron centre with a structure not previously observed in proteins; it resembles a hybrid of the iron centres of heme and Fe-S proteins. The low-spin electronic configuration presumably results in part from two Fe-amide nitrogen bonds. The structure is consistent with the metal ion having a role as a Lewis acid in the catalytic reaction.

Selected figure(s)

Figure 2.
Figure 2. Subunit topology and structure of nitrile hydratase. (a) Topology diagram for the a and b subunits of nitrile hydratase. The a subunit is shown in blue and the b subunit in yellow. The location of the iron centre is indicated by a red sphere. (b) Schematic view of the a subunit. (c) Schematic view of the b subunit. Figures (b) and (c) were generated with the programs Molscript [36] and Raster3D [37].

The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 691-699) copyright 1997.

Figure was selected by an automated process.