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Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site.

Ladner JE, Obmolova G, Teplyakov A, Howard AJ, Khil PP, Camerini-Otero RD, Gilliland GL - BMC Struct. Biol. (2003)

Bottom Line: The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.The 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.

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Affiliation: Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA. jane.ladner@nist.gov

ABSTRACT

Background: The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.

Results: The 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.

Conclusion: The 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.

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A view looking down into the toroid at the putative active site. A gap between the dimers and a trough lead down toward the site. Where conserved residues contact the surface, the surface has been colored red. Again the metal ions are depicted as silver balls. This figure was prepared using PyMol [34].
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Figure 4: A view looking down into the toroid at the putative active site. A gap between the dimers and a trough lead down toward the site. Where conserved residues contact the surface, the surface has been colored red. Again the metal ions are depicted as silver balls. This figure was prepared using PyMol [34].

Mentions: The highly conserved residues of the DUF34 family are concentrated in two regions of the ybgI structure: at the putative active site and on the side of a groove between the polypeptide chains of the trimer. Figure 4 shows the conserved residues mapped onto the surface of the molecule.


Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site.

Ladner JE, Obmolova G, Teplyakov A, Howard AJ, Khil PP, Camerini-Otero RD, Gilliland GL - BMC Struct. Biol. (2003)

A view looking down into the toroid at the putative active site. A gap between the dimers and a trough lead down toward the site. Where conserved residues contact the surface, the surface has been colored red. Again the metal ions are depicted as silver balls. This figure was prepared using PyMol [34].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC239858&req=5

Figure 4: A view looking down into the toroid at the putative active site. A gap between the dimers and a trough lead down toward the site. Where conserved residues contact the surface, the surface has been colored red. Again the metal ions are depicted as silver balls. This figure was prepared using PyMol [34].
Mentions: The highly conserved residues of the DUF34 family are concentrated in two regions of the ybgI structure: at the putative active site and on the side of a groove between the polypeptide chains of the trimer. Figure 4 shows the conserved residues mapped onto the surface of the molecule.

Bottom Line: The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA. jane.ladner@nist.gov

ABSTRACT

Background: The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.

Results: The 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.

Conclusion: The 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.

Show MeSH