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Published online before print March 1, 2005, 10.1110/ps.041183305
Protein Science (2005), 14:1004-1010. Published by Cold Spring Harbor Laboratory Press. Copyright © 2005 The Protein Society
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Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8

Noriko Handa1, Takaho Terada1,2, Yukiko Doi-Katayama1, Hiroshi Hirota1,3, Jeremy R.H. Tame4, Sam-Yong Park4, Seiki Kuramitsu2,5, Mikako Shirouzu1,2 and Shigeyuki Yokoyama1,2,6

1 RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan2 RIKEN Harima Institute at SPring-8, Sayo-gun, Hyogo 679-5148, Japan3 Protein Folds Research Laboratory, Graduate School of Integrated Science and 4 Protein Design Laboratory, Graduate School of Integrated Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan5 Department of Biology, Graduate School of Science, Osaka University, Osaka 560-0043, Japan6 Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan

(RECEIVED October 21, 2004; FINAL REVISION December 1, 2004; ACCEPTED December 1, 2004)

The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. Here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, TT1927b, from Thermus thermophilus HB8, complexed with its ligand. This protein belongs to the YceI-like family in the Pfam database, and its sequence homologs are present in a broad range of bacteria and archaea. The structure consists of an extended, eight-stranded, antiparallel {beta}-barrel. In the hydrophobic pore of the barrel, the protein binds the polyisoprenoid chain by hydrophobic interactions. Its overall structure resembles the lipocalin fold, but there is no sequence homology between TT1927b and the lipocalin family of proteins.

Keywords: Thermus thermophilus HB8; polyisoprenoid-binding protein; crystallography; YceI-like family; eight-stranded {beta}-barrel

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041183305.

Reprint requests to: Shigeyuki Yokoyama, Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; e-mail: yokoyama{at}biochem.s.u-tokyo.ac.jp; fax: +81-45-503-9195.


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