The 1.9 angstrom crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results

Rubrerythrin is a non-heme iron dimeric protein isolated from the sulfate-r educing 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 Angstrom 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 nat ive "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 s ame general protein fold, domain structure, and dimeric interactions as pre viously found for rubrerythrin [1, 2], but it also has some interesting und etected differences at the metal centers. The refined model of the protein structure has a cis peptide between residues 78 and 79. The Fe-Cys(4) cente r has a previously undetected strong seventh N-H ... S hydrogen bond in add ition 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. E ach metal is coordinated by a GluXXHis polypeptide chain segment. The Zn at om binds at a site distinctly different: from that found in the structure o f a diiron rubrerythrin. Difference electron density for the uranyl derivat ive shows an extremely large peak adjacent to and replacing the Zn atom, in dicating 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.