PDBsum entry: 1j9r

Oxidoreductase

PDB id: 1j9r

Contents

Protein chains

336 a.a. *

Ligands

NO2 ×3

Metals

_CU ×9

Waters ×1099

* Residue conservation analysis

PDB id:

1j9r

Name:

Oxidoreductase

Title:

Crystal structure of nitrite soaked reduced d98n afnir

Structure:

Copper-containing nitrite reductase. Chain: a, b, c. Fragment: residues 40-376. Synonym: cu-nir. Engineered: yes. Mutation: yes

Source:

Alcaligenes faecalis. Organism_taxid: 511. Strain: s-6. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.00Å R-factor: 0.186 R-free: 0.225

Authors:

M.J.Boulanger,M.E.Murphy

Key ref:

M.J.Boulanger and M.E.Murphy (2001). Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate. Biochemistry, 40, 9132-9141. PubMed id: 11478880 DOI: 10.1021/bi0107400

Date:

28-May-01 Release date: 06-Jun-01

Protein chains

P38501  (NIR_ALCFA) -  Copper-containing nitrite reductase

Seq: 376 a.a.

Struc: 336 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.7.2.1 - Nitrite reductase (NO-forming).
• Reaction: Nitric oxide + H₂O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H⁺

Nitric oxide + H(2)O + ferricytochrome c = nitrite (Bound ligand (Het Group name = NO2) corresponds exactly) + ferrocytochrome c + 2 × H(+)

• Cofactor: Copper or iron; FAD

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

 Gene Ontology (GO) functional annotation 

• Cellular component: periplasmic space (1 term)
• Biological process: nitrogen compound metabolic process (3 terms)
• Biochemical function: oxidoreductase activity (4 terms)

reference

DOI no: 10.1021/bi0107400

Biochemistry 40:9132-9141 (2001)

PubMed id: 11478880

Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate.

M.J.Boulanger, M.E.Murphy.

ABSTRACT

High-resolution nitrite soaked oxidized and reduced crystal structures of two active site mutants, D98N and H255N, of nitrite reductase (NIR) from Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution. In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to the type II copper via its oxygen atoms in an asymmetric bidentate manner; however, elevated B-factors and weak electron density indicate that both nitrite and Asn98 are less ordered than in the native enzyme. This disorder likely results from the inability of the N delta 2 atom of Asn98 to form a hydrogen bond with the bound protonated nitrite, indicating that the hydrogen bond between Asp98 and nitrite in the native NIR structure is essential in anchoring nitrite in the active site for catalysis. In the oxidized nitrite soaked H255N crystal structure, nitrite does not displace the ligand water and is instead coordinated in an alternative mode via a single oxygen to the type II copper. His255 is clearly essential in defining the nitrite binding site despite the lack of direct interaction with the substrate in the native enzyme. The resulting pentacoordinate copper site in the H255N structure also serves as a model for a proposed transient intermediate in the catalytic mechanism consisting of a hydroxyl and nitric oxide molecule coordinated to the copper. The formation of an unusual dinuclear type I copper site in the reduced nitrite soaked D98N and H255N crystal structures may represent an evolutionary link between the mononuclear type I copper centers and dinuclear Cu(A) sites.