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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.

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.

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The crystal structure of ybgI from E. coli. (A) Stereo view of the secondary structure cartoon showing the fold of the polypeptide chain. Domain 1 is shown with helices in blue and ß-strands in red and domain 2 is shown with helices in cyan and ß-strands in rose. The strands and helices are numbered sequentially from the N-terminus. This figure was prepared using MOLSCRIPT [31] and Raster3D [32,33]. (B) Topology diagram of the secondary structure. Helicies are represented as rectangles and ß-strands are represented as arrows.
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Figure 1: The crystal structure of ybgI from E. coli. (A) Stereo view of the secondary structure cartoon showing the fold of the polypeptide chain. Domain 1 is shown with helices in blue and ß-strands in red and domain 2 is shown with helices in cyan and ß-strands in rose. The strands and helices are numbered sequentially from the N-terminus. This figure was prepared using MOLSCRIPT [31] and Raster3D [32,33]. (B) Topology diagram of the secondary structure. Helicies are represented as rectangles and ß-strands are represented as arrows.

Mentions: The ybgI protein consists of two similar interlinked a/ß domains; both are 3-layer sandwiches (alpha-beta-alpha) as shown in Figure 1. The first domain has a 5-stranded mixed ß-sheet with two a-helices on one side and three a-helices on the other side. Two of the three a-helices are approximately parallel to the ß-strands of the ß-sheet and the third is shorter, approximately perpendicular to the ß-strands and leads over to the second domain. The order of the ß-strands is 1-4-3-2-11. The second domain also has a central mixed ß-sheet but has 6 ß-strands with the order 5-6-8-9-10-7; the ß-sheet is flanked on each side by two a-helices and there is an additional short a-helix leading back to domain 1. The crystallographic asymmetric unit contains three dimers. The application of the three-fold crystal symmetry reveals that the quaternary structure is a toroid formed by three crystallographically related dimers. In the crystals, these toroids stack forming long tubes. The toroidal structure is shown in Figures 2A and 2B.


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)

The crystal structure of ybgI from E. coli. (A) Stereo view of the secondary structure cartoon showing the fold of the polypeptide chain. Domain 1 is shown with helices in blue and ß-strands in red and domain 2 is shown with helices in cyan and ß-strands in rose. The strands and helices are numbered sequentially from the N-terminus. This figure was prepared using MOLSCRIPT [31] and Raster3D [32,33]. (B) Topology diagram of the secondary structure. Helicies are represented as rectangles and ß-strands are represented as arrows.
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Related In: Results  -  Collection

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Figure 1: The crystal structure of ybgI from E. coli. (A) Stereo view of the secondary structure cartoon showing the fold of the polypeptide chain. Domain 1 is shown with helices in blue and ß-strands in red and domain 2 is shown with helices in cyan and ß-strands in rose. The strands and helices are numbered sequentially from the N-terminus. This figure was prepared using MOLSCRIPT [31] and Raster3D [32,33]. (B) Topology diagram of the secondary structure. Helicies are represented as rectangles and ß-strands are represented as arrows.
Mentions: The ybgI protein consists of two similar interlinked a/ß domains; both are 3-layer sandwiches (alpha-beta-alpha) as shown in Figure 1. The first domain has a 5-stranded mixed ß-sheet with two a-helices on one side and three a-helices on the other side. Two of the three a-helices are approximately parallel to the ß-strands of the ß-sheet and the third is shorter, approximately perpendicular to the ß-strands and leads over to the second domain. The order of the ß-strands is 1-4-3-2-11. The second domain also has a central mixed ß-sheet but has 6 ß-strands with the order 5-6-8-9-10-7; the ß-sheet is flanked on each side by two a-helices and there is an additional short a-helix leading back to domain 1. The crystallographic asymmetric unit contains three dimers. The application of the three-fold crystal symmetry reveals that the quaternary structure is a toroid formed by three crystallographically related dimers. In the crystals, these toroids stack forming long tubes. The toroidal structure is shown in Figures 2A and 2B.

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