PDBsum entry 1vzi

Oxidoreductase

PDB id: 1vzi

Contents

Protein chains

125 a.a. *

Ligands

_CL ×4

Metals

FE2 ×4

_CA ×2

Waters ×518

* Residue conservation analysis

PDB id:

1vzi

Name:

Oxidoreductase

Title:

Structure of superoxide reductase bound to ferrocyanide and active site expansion upon x-ray induced photoreduction

Structure:

Desulfoferrodoxin. Chain: a, b. Synonym: superoxide reductase, dfx, sor. Engineered: yes. Mutation: yes

Source:

Desulfovibrio baarsii. Organism_taxid: 453230. Expressed in: escherichia coli dh5[alpha]. Expression_system_taxid: 668369.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.15Å R-factor: 0.143

Authors:

V.Adam,A.Royant,V.Niviere,F.P.Molina-Heredia,D.Bourgeois

Key ref:

V.Adam et al. (2004). Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction. Structure, 12, 1729-1740. PubMed id: 15341736 DOI: 10.1016/j.str.2004.07.013

Date:

19-May-04 Release date: 27-Aug-04

Protein chains

Q46495  (DFX_DESB2) -  Desulfoferrodoxin from Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / LMG 7858 / VKM B-1802 / 2st14)

Seq: 126 a.a.

Struc: 125 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.15.1.2 - superoxide reductase.
• Reaction: reduced [rubredoxin] + superoxide + 2 H⁺ = oxidized [rubredoxin] + H2O2
• Cofactor: Fe cation

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

Key reference

DOI no: 10.1016/j.str.2004.07.013

Structure 12:1729-1740 (2004)

PubMed id: 15341736

Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction.

V.Adam, A.Royant, V.Nivière, F.P.Molina-Heredia, D.Bourgeois.

ABSTRACT

Some sulfate-reducing and microaerophilic bacteria rely on the enzyme superoxide reductase (SOR) to eliminate the toxic superoxide anion radical (O2*-). SOR catalyses the one-electron reduction of O2*- to hydrogen peroxide at a nonheme ferrous iron center. The structures of Desulfoarculus baarsii SOR (mutant E47A) alone and in complex with ferrocyanide were solved to 1.15 and 1.7 A resolution, respectively. The latter structure, the first ever reported of a complex between ferrocyanide and a protein, reveals that this organo-metallic compound entirely plugs the SOR active site, coordinating the active iron through a bent cyano bridge. The subtle structural differences between the mixed-valence and the fully reduced SOR-ferrocyanide adducts were investigated by taking advantage of the photoelectrons induced by X-rays. The results reveal that photo-reduction from Fe(III) to Fe(II) of the iron center, a very rapid process under a powerful synchrotron beam, induces an expansion of the SOR active site.

Selected figure(s)

Figure 2.
Figure 2. Details of the SOR Active SiteFinal 2F[o] - F[c] electron density map, contoured at 1.0 s, superimposed onto a ball-and-stick representation of the active site. Center II iron and chloride are represented as dark green and lime green spheres, respectively. Iron coordination is shown by purple dotted lines. The chloride anion binds tightly only in monomer A, where Lys48 is highly ordered. In monomer B, a crystalline contact partially disorders Lys48, thus disrupting the water network at this location and leading to alternate positions for the chloride ion, as suggested by an elongated electron density (data not shown). Figures 2, 5B, 5C, 6, and 7 were prepared with Bobscript (Esnouf, 1999) and Raster 3D (Merritt and Bacon, 1997).

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1729-1740) copyright 2004.

Figure was selected by an automated process.