PDBsum entry: 1s2z

Electron transport

PDB id: 1s2z

Contents

Protein chain

190 a.a. *

Metals

_FE ×2

_ZN

Waters ×239

* Residue conservation analysis

PDB id:

1s2z

Name:

Electron transport

Title:

X-ray crystal structure of desulfovibrio vulgaris rubrerythr displacement of iron by zinc at the diiron site

Structure:

Rubrerythrin. Chain: a. Engineered: yes

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

1.75Å R-factor: 0.178 R-free: 0.196

Authors:

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

Key ref:

S.Jin et al. (2004). Displacement of iron by zinc at the diiron site of Desulfovibrio vulgaris rubrerythrin: X-ray crystal structure and anomalous scattering analysis. J Inorg Biochem, 98, 786-796. PubMed id: 15134924 DOI: 10.1016/j.jinorgbio.2004.01.005

Date:

12-Jan-04 Release date: 22-Jun-04

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: 10.1016/j.jinorgbio.2004.01.005

J Inorg Biochem 98:786-796 (2004)

PubMed id: 15134924

Displacement of iron by zinc at the diiron site of Desulfovibrio vulgaris rubrerythrin: X-ray crystal structure and anomalous scattering analysis.

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

ABSTRACT

X-ray crystal structures of recombinant Desulfovibrio (D.) vulgaris rubrerythrin (Rbr) have shown a diiron site, whereas the crystal structure of Rbr "as-isolated" from D. vulgaris was reported to contain a mixed Zn,Fe binuclear site. To investigate the possibility that zinc had displaced iron during isolation or crystallization of the "as-isolated" D. vulgaris Rbr, the X-ray crystal structure of recombinant D. vulgaris all-iron Rbr that had been incubated with excess zinc sulfate prior to crystallization, yielding a protein labeled Zn,FeRbr, was solved. Analysis of the anomalous scattering data obtained at two different wavelengths showed that zinc had displaced a significant proportion of iron from both iron centers of the diiron site, and site. UV-visible absorption spectra of the redissolved Zn,FeRbr crystals showed 30-40% retention of oxo-bridged diferric sites, and the redissolved crystals had 37% of the peroxidase specific activity of the starting all-iron Rbr, which, together with the crystallographic results, indicate a predominant mixture of Fe1,Fe2 and Zn1,Zn2 sites. The structure of the Zn(Fe)1,Fe(Zn)2 binuclear site in the Zn,FeRbr crystals was very similar to that of the Zn,Fe binuclear site reported for the "as-isolated" D. vulgaris Rbr, including tetrahedral four-coordination at the Zn(Fe)1 site. The diiron sites in the recombinant Zn,FeRbr crystals were likely at least partially reduced during synchrotron irradiation. Our results suggest that the mixed-metal binuclear site reported for the "as-isolated" D. vulgaris Rbr could be due to displacement of iron from a native diiron site by adventitious zinc during isolation and/or crystallization, and that reduced diiron and dizinc sites can adopt very similar structures in Rbr.