PDBsum entry: 1lkm

Electron transport

PDB id: 1lkm

Contents

Protein chain

190 a.a. *

Metals

_FE ×3

Waters ×230

* Residue conservation analysis

PDB id:

1lkm

Name:

Electron transport

Title:

Crystal structure of desulfovibrio vulgaris rubrerythrin all form

Structure:

Rubrerythrin all-iron(iii) form. Chain: a. Engineered: yes

Source:

Desulfovibrio vulgaris. Organism_taxid: 881. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.69Å R-factor: 0.190 R-free: 0.210

Authors:

S.Jin,D.M.Kurtz Jr.,Z.J.Liu,J.Rose,B.C.Wang

Key ref:

S.Jin et al. (2002). X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase. J Am Chem Soc, 124, 9845-9855. PubMed id: 12175244 DOI: 10.1021/ja026587u

Date:

25-Apr-02 Release date: 18-Sep-02

Protein chain

P24931  (RUBY_DESVH) -  Rubrerythrin

Seq: 191 a.a.

Struc: 190 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: cellular_component (2 terms)
• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: oxidoreductase activity (4 terms)

DOI no: 10.1021/ja026587u

J Am Chem Soc 124:9845-9855 (2002)

PubMed id: 12175244

X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase.

S.Jin, D.M.Kurtz, Z.J.Liu, J.Rose, B.C.Wang.

ABSTRACT

Rubrerythrin (Rbr) is a 44-kDa homodimeric protein, found in many air-sensitive bacteria and archaea, which contains a unique combination of a rubredoxin-like site and a non-sulfur, oxo/dicarboxylato-bridged diiron site. The diiron site structure resembles those found in O2-activating diiron enzymes. However, Rbr instead appears to function as a hydrogen peroxide reductase (peroxidase). The diferrous site in all-ferrous Rbr (Rbr(red)) shows a much greater reactivity with H2O2 than does the diferric site in all-ferric Rbr (Rbr(ox)), but only the latter structure has been reported. Here we report the X-ray crystal structures of the recombinant Rbr(red) from the sulfate reducing bacterium, Desulfovibrio vulgaris, as well as its azide adduct (Rbr(red)N3). We have also redetermined the structure of Rbr(ox) to a higher resolution than previously reported. The structural differences between Rbr(ox) and Rbr(red) are localized entirely at the diiron site. The most striking structural change upon reduction of the diferric to the diferrous site of Rbr is a 1.8-A movement of one iron away from a unique glutamate carboxylate ligand and toward a trans-disposed histidine side chain, which replaces the glutamate as a ligand. This movement increases the inter-iron distance from 3.3 to 4 A. Rbr(red)N(3) shows this same iron movement and His-->Glu ligand replacement relative to Rbr(ox), and, in addition, an azide coordinated to the diiron site in a cis mu-1,3 fashion, replacing two solvent ligands in Rbr(red). Relative to those in O2-activating enzymes, the bridging carboxylate ligation of the Rbr diiron site is less flexible upon diferric/diferrous interconversion. The diferrous site is also much more rigid, symmetrical, and solvent-exposed than those in O2-activating enzymes. On the basis of these unique structural features, a mechanism is proposed for facile reduction of hydrogen peroxide by Rbr involving a cis mu-eta(2) H2O2 diferrous intermediate.