PDBsum entry 4zk8

Oxidoreductase

PDB id: 4zk8

Contents

Protein chain

294 a.a.

Ligands

MPD ×3

PEG

EDO

SO4

ACY ×2

TRS

Metals

_CU ×18

_CL ×2

Waters ×403

PDB id:

4zk8

Name:

Oxidoreductase

Title:

Copper-containing nitrite reductase from thermophilic bacterium geobacillus thermodenitrificans (re-refined)

Structure:

Nitrite reductase. Chain: a. Fragment: unp residues 31-352. Synonym: copper nitrite reductase. Engineered: yes

Source:

Geobacillus thermodenitrificans ng80-2. Organism_taxid: 420246. Strain: ng80-2. Gene: nirk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.15Å R-factor: 0.122 R-free: 0.146

Authors:

Y.Fukuda,T.Inoue

Key ref:

Y.Fukuda et al. (2014). Structural insights into the function of a thermostable copper-containing nitrite reductase. J Biochem (tokyo), 155, 123-135. PubMed id: 24293549 DOI: 10.1093/jb/mvt107

Date:

30-Apr-15 Release date: 20-May-15

Supersedes:

3wko

Protein chain

A4IL26  (A4IL26_GEOTN) -  Copper-containing nitrite reductase from Geobacillus thermodenitrificans (strain NG80-2)

Seq: 352 a.a.

Struc: 294 a.a.

Enzyme reactions

• Enzyme class: E.C.1.7.2.1 - nitrite reductase (NO-forming).
• Reaction: nitric oxide + Fe(III)-[cytochrome c] + H2O = Fe(II)-[cytochrome c] + nitrite + 2 H⁺
• Cofactor: Cu cation or Fe cation; FAD

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

reference

DOI no: 10.1093/jb/mvt107

J Biochem (tokyo) 155:123-135 (2014)

PubMed id: 24293549

Structural insights into the function of a thermostable copper-containing nitrite reductase.

Y.Fukuda, K.M.Tse, M.Lintuluoto, Y.Fukunishi, E.Mizohata, H.Matsumura, H.Takami, M.Nojiri, T.Inoue.

ABSTRACT

Copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO(-)2) to nitric oxide (NO) during denitrification. We determined the crystal structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus thermodenitrificans (GtNIR) in chloride- and formate-bound forms of wild type at 1.15 Å resolution and the nitrite-bound form of the C135A mutant at 1.90 Å resolution. The structure of C135A with nitrite displays a unique η(1)-O coordination mode of nitrite at the catalytic copper site (T2Cu), which has never been observed at the T2Cu site in known wild-type CuNIRs, because the mobility of two residues essential to catalytic activity, Asp98 and His244, are sterically restricted in GtNIR by Phe109 on a characteristic loop structure that is found above Asp98 and by an unusually short CH-O hydrogen bond observed between His244 and water, respectively. A detailed comparison of the WT structure with the nitrite-bound C135A structure implies the replacement of hydrogen-bond networks around His244 and predicts the flow path of protons consumed by nitrite reduction. On the basis of these observations, the reaction mechanism of GtNIR through the η(1)-O coordination manner is proposed.