Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD

doi:10.1110/ps.062148506

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Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 Å resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD

Kaori Ito¹^,5, Ryoichi Arai¹^,2^,5, Emiko Fusatomi¹, Tomomi Kamo-Uchikubo¹, Shin-Ichi Kawaguchi², Ryogo Akasaka¹, Takaho Terada¹^,2, Seiki Kuramitsu²^,3, Mikako Shirouzu¹^,2 and Shigeyuki Yokoyama¹^,2^,4

¹ Protein Research Group, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan
² RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo 679-5148, Japan
³ Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
⁴ Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan

(RECEIVED February 10, 2006; FINAL REVISION February 10, 2006; ACCEPTED February 16, 2006)

TTHA0727 is a conserved hypothetical protein from Thermus thermophilusHB8, with a molecular mass of 12.6 kDa. TTHA0727 belongs tothe carboxymuconolactone decarboxylase (CMD) family (Pfam 02627).A sequence comparison with its homologs suggested that TTHA0727is a distinct protein from alkylhydroperoxidase AhpD and ${gamma}$ -carboxymuconolactonedecarboxylase in the CMD family. Here we report the 1.9 Åcrystal structure of TTHA0727 (PDB ID: 2CWQ) determined by themultiwavelength anomalous dispersion method. The TTHA0727 monomerstructure consists of seven ${alpha}$ -helices ( ${alpha}$ 1– ${alpha}$ 7) and one short3₁₀-helix. The crystal structure and the analytical ultracentrifugationrevealed that TTHA0727 forms a hexameric ring structure in solution.The electrostatic potential distribution on the solvent-accessiblesurface of the TTHA0727 hexamer showed that positively chargedregions exist on the side of the ring structure, suggestingthat TTHA0727 interacts with some negatively charged molecules.A structural homology search revealed that the structure ofthree ${alpha}$ -helices ( ${alpha}$ 4– ${alpha}$ 6) is remarkably conserved, suggestingthat it is the common structural motif for the CMD family proteins.In addition, the nine residues of the N-terminal tag bound tothe cleft region between ${alpha}$ 1 and ${alpha}$ 3 in chains A and B of TTHA0727,implying that this region is the putative binding/active sitefor some small molecules.

Keywords: extremely thermophilic bacteria; Thermus thermophilus HB8; hypothetical protein; TTHA0727 (TT1628); carboxymuconolactone decarboxylase (CMD) family; hexameric ring structure; structural genomics/proteomics

⁵ These authors contributed equally to this work.

Supplemental material see www.proteinscience.org

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

Article published online ahead of print. Article and publicationdate are at http://www.proteinscience.org/cgi/doi/10.1110/ps.062148506.

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