PDBsum entry 1snr

Oxidoreductase

PDB id: 1snr

Contents

Protein chains

336 a.a. *

Ligands

ACT ×8

_NO ×3

TRS

Metals

CU1 ×3

_CU ×3

Waters ×1099

* Residue conservation analysis

PDB id:

1snr

Name:

Oxidoreductase

Title:

Nitric oxide bound to cu nitrite reductase

Structure:

Copper-containing nitrite reductase. Chain: a, b, c. Synonym: cu-nir. Engineered: yes

Source:

Alcaligenes faecalis. Organism_taxid: 511. Gene: nirk, nir. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

1.31Å R-factor: 0.125 R-free: 0.141

Authors:

E.I.Tocheva,F.I.Rosell,A.G.Mauk,M.E.Murphy

Key ref:

E.I.Tocheva et al. (2004). Side-on copper-nitrosyl coordination by nitrite reductase. Science, 304, 867-870. PubMed id: 15131305 DOI: 10.1126/science.1095109

Date:

11-Mar-04 Release date: 22-Jun-04

Protein chains

P38501  (NIR_ALCFA) -  Copper-containing nitrite reductase from Alcaligenes faecalis

Seq: 376 a.a.

Struc: 337 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⁺

nitric oxide + Fe(III)-[cytochrome c] + H2O (Bound ligand (Het Group name = NO) corresponds exactly) = 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: 10.1126/science.1095109

Science 304:867-870 (2004)

PubMed id: 15131305

Side-on copper-nitrosyl coordination by nitrite reductase.

E.I.Tocheva, F.I.Rosell, A.G.Mauk, M.E.Murphy.

ABSTRACT

A copper-nitrosyl intermediate forms during the catalytic cycle of nitrite reductase, the enzyme that mediates the committed step in bacterial denitrification. The crystal structure of a type 2 copper-nitrosyl complex of nitrite reductase reveals an unprecedented side-on binding mode in which the nitrogen and oxygen atoms are nearly equidistant from the copper cofactor. Comparison of this structure with a refined nitrite-bound crystal structure explains how coordination can change between copper-oxygen and copper-nitrogen during catalysis. The side-on copper-nitrosyl in nitrite reductase expands the possibilities for nitric oxide interactions in copper proteins such as superoxide dismutase and prions.

Selected figure(s)

Figure 1.
Fig. 1. Stereo views of the type 2 Cu sites with (A) bound nitrite and (B) nitric oxide. In each panel, the electron density represented in gray is a 2F[o] - F[c] map contoured at 0.55 e^-/Å3 (1.2 for each structure). Omit difference maps of the nitrite and nitric oxide ligands are colored in green and contoured at 0.6 e^-/Å3 (5.1 for NO[2]^- and 4.6 for NO). Carbons (orange), oxygens (red), nitrogens (blue), type 2 Cu (brown), and waters (cyan) are colored as indicated. (C) Overview of the essential features of the active sites of NiR bound with nitrite (left) and with nitric oxide (right). Metal-ligand bonds (solid), as well as H bonds and other electrostatic interactions (dashed), are shown as gray lines of the type indicated.

Figure 3.
Fig. 3. Revised mechanism of Cu-containing nitrite reductase.

The above figures are reprinted by permission from the AAAs: Science (2004, 304, 867-870) copyright 2004.

Figures were selected by the author.