PDBsum entry: 1fwx

Oxidoreductase

PDB id: 1fwx

Contents

Protein chains

591 a.a. *

Ligands

CUA ×4

CUZ ×4

Metals

_CL ×4

_CA ×11

Waters ×2642

* Residue conservation analysis

PDB id:

1fwx

Name:

Oxidoreductase

Title:

Crystal structure of nitrous oxide reductase from p. Denitri

Structure:

Nitrous oxide reductase. Chain: a, b, c, d. Ec: 1.7.99.6

Source:

Paracoccus denitrificans. Organism_taxid: 266

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.241 R-free: 0.264

Authors:

K.Brown,K.Djinovic-Carugo,T.Haltia,I.Cabrito,M.Saraste,J.J.M I.Moura,M.Tegoni,C.Cambillau

Key ref:

K.Brown et al. (2000). Revisiting the catalytic CuZ cluster of nitrous oxide (N2O) reductase. Evidence of a bridging inorganic sulfur. J Biol Chem, 275, 41133-41136. PubMed id: 11024061 DOI: 10.1074/jbc.M008617200

Date:

25-Sep-00 Release date: 25-Sep-01

Protein chains

Q51705  (NOSZ_PARDE) -  Nitrous-oxide reductase

Seq: 652 a.a.

Struc: 591 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.7.2.4 - Nitrous-oxide reductase.
• Reaction: Nitrogen + H₂O + 2 cytochrome c = nitrous oxide + 2 reduced cytochrome c
• Cofactor: Copper

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (2 terms)
• Biological process: oxidation-reduction process (1 term)
• Biochemical function: protein binding (7 terms)

reference

DOI no: 10.1074/jbc.M008617200

J Biol Chem 275:41133-41136 (2000)

PubMed id: 11024061

Revisiting the catalytic CuZ cluster of nitrous oxide (N2O) reductase. Evidence of a bridging inorganic sulfur.

K.Brown, K.Djinovic-Carugo, T.Haltia, I.Cabrito, M.Saraste, J.J.Moura, I.Moura, M.Tegoni, C.Cambillau.

ABSTRACT

Nitrous-oxide reductases (N2OR) catalyze the two-electron reduction of N(2)O to N(2). The crystal structure of N2ORs from Pseudomonas nautica (Pn) and Paracoccus denitrificans (Pd) were solved at resolutions of 2.4 and 1.6 A, respectively. The Pn N2OR structure revealed that the catalytic CuZ center belongs to a new type of metal cluster in which four copper ions are liganded by seven histidine residues. A bridging oxygen moiety and two other hydroxide ligands were proposed to complete the ligation scheme (Brown, K., Tegoni, M., Prudencio, M., Pereira, A. S., Besson, S., Moura, J. J. G., Moura, I., and Cambillau, C. (2000) Nat. Struct. Biol. 7, 191-195). However, in the CuZ cluster, inorganic sulfur chemical determination and the high resolution structure of Pd N2OR identified a bridging inorganic sulfur instead of an oxygen. This result reconciles the novel CuZ cluster with the hitherto puzzling spectroscopic data.

Selected figure(s)

Figure 1.
Fig. 1. Pn N2OR, the N[2]O reductase from P. nautica. An overall view of the crystal structure of the N2OR dimer is shown; one monomer is uniformly colored gray, whereas for the other monomer the propeller domain -strands are dark green and the -helices light green, the linker is purple, and the -strands of the cupredoxin domain are blue or red according to the -sheet they form; the short 3[10] helix adjacent to the CuA center is dark blue (figure prepared with MOLSCRIPT (19)).

Figure 2.
Fig. 2. Stereo representation of the CuZ center from P. denitrificans N[2]O reductase. A, the CuZ in its 2F[o] F[c] SigmaA electron density contoured at the 1.2 (blue) and 8 level (red). An F[o] F[c]SigmaA omit electron density map is represented around the CuZ sulfur atom, contoured at 10 (dark blue). Copper is dark blue, the bridging inorganic sulfur is green, the oxygen ligand is red, imidazole rings from the histidines are atom color-coded. B, side view, about 90° around a vertical axis. C, the F[o] F[c] SigmaA omit electron density maps of the CuZ cluster and Met470 are contoured at the 8 and 12 levels (red and dark blue, respectively). The atomic occupancies of the sulfur atoms have been set to 0, and Pd N2OR has been subjected to a short cartesian annealing refinement (figure prepared with TURBO-FRODO (15)).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 41133-41136) copyright 2000.

Figures were selected by an automated process.