1dvb

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Revision as of 11:29, 20 November 2007

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spinqualitylabelsall models 1dvb, resolution 1.9Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

RUBRERYTHRIN

Overview

Rubrerythrin is a non-heme iron dimeric protein isolated from the, sulfate-reducing bacterium Desulfovibrio vulgaris. Each monomer has one, mononuclear iron center similar to rubredoxin and one dinuclear metal, center similar to hemerythrin or ribonucleotide reductase. The 1.88 A, X-ray structure of the "as isolated" molecule and a uranyl heavy atom, derivative have been solved by molecular replacement techniques. The, resulting model of the native "as isolated" molecule, including 164 water, molecules, has been refined giving a final R factor of 0.197 (R(free) =, 0.255). The structure has the same general protein fold, domain structure, and dimeric interactions as previously found for rubrerythrin [1, 2], but, it also has some interesting undetected differences at the metal centers., The refined model of the protein structure has a cis peptide between, residues 78 and 79. The Fe-Cys4 center has a previously undetected strong, seventh N-H...S hydrogen bond in addition to the six N-H...S bonds usually, found in rubredoxin. The dinuclear metal center has a hexacoordinate Fe, atom and a tetracoordinate Zn atom. Each metal is coordinated by a, GluXXHis polypeptide chain segment. The Zn atom binds at a site distinctly, different from that found in the structure of a diiron rubrerythrin., Difference electron density for the uranyl derivative shows an extremely, large peak adjacent to and replacing the Zn atom, indicating that this, particular site is capable of binding other atoms. This feature/ability, may give rise to some of the confusing activities ascribed to this, molecule.

About this Structure

1DVB is a Single protein structure of sequence from Desulfovibrio vulgaris with FE and ZN as ligands. Full crystallographic information is available from OCA.

Reference

The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results., Sieker LC, Holmes M, Le Trong I, Turley S, Liu MY, LeGall J, Stenkamp RE, J Biol Inorg Chem. 2000 Aug;5(4):505-13. PMID:10968622

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