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Abstract

BackgroundThe protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.ResultsThe structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid.ConclusionThe toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.

Escherichia coli Genes and Pathways Involved in Surviving Extreme Exposure to Ionizing Radiation

“…Of the eight genes, three have homologs identified in all three domains of life, and all eight have homologs in eukaryotes. In no instance has the function of one of these homologs been described in detail, although some hints about YbjN, YebC, YejH, and YbgI functions have appeared (76,77,87,88). In several cases, we provide here the first phenotype described for cells lacking the functions of these genes.…”

“…It is a toroidal structure consisting of a trimer of dimers, wherein each subunit exhibits two metal binding sites on the inside of the toroid (76). The ybgI gene shares an operon with the gene that encodes endonuclease VIII, eliciting some speculation about a possible DNA repair function (76). The product of the yebC gene appears to have a function in the transcriptional regulation of the RuvABC proteins, which are all involved in recombinational DNA repair (77).…”

“…Although the function remains enigmatic, the structure of the YbgI protein is known. It is a toroidal structure consisting of a trimer of dimers, wherein each subunit exhibits two metal binding sites on the inside of the toroid (76). The ybgI gene shares an operon with the gene that encodes endonuclease VIII, eliciting some speculation about a possible DNA repair function (76).…”

Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures

“…The clusters delineate a putative binding site that occupies the same position as the Flavin mononucleotide molecule (shown) in the structurally similar Rv1155 pyridoxine 5′-phosphate oxidase [52]. b Structure of Escherichia coli protein ybgI (PDB code: 1nmo [53]) showing a large OP probe cluster identified using the single-linkage clustering algorithm in SiteHound. This large cluster would seem to be compatible with a suggested role of ybgI in DNA metabolism [53]…”

“…b Structure of Escherichia coli protein ybgI (PDB code: 1nmo [53]) showing a large OP probe cluster identified using the single-linkage clustering algorithm in SiteHound. This large cluster would seem to be compatible with a suggested role of ybgI in DNA metabolism [53]…”