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Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8

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Journal of Structural and Functional Genomics

Abstract

The TT1485 gene from Thermus thermophilus HB8 encodes a hypothetical protein of unknown function with about 20 sequence homologs of bacterial or archaeal origin. Together they form a family of uncharacterized proteins, the cluster of orthologous group COG3253. Using a combination of amino acid sequence analysis, three-dimensional structural studies and biochemical assays, we identified TT1485 as a novel heme-binding protein. The crystal structure reveals that this protein is a pentamer and each monomer exhibits a β-barrel fold. TT1485 is structurally similar to muconolactone isomerase, but this provided no functional clues. Amino acid sequence analysis revealed remote homology to a heme enzyme, chlorite dismutase. Strikingly, amino acid residues that are highly conserved in the homologous hypothetical proteins and chlorite dismutase cluster around a deep cavity on the surface of each monomer. Molecular modeling shows that the cavity can accommodate a heme group with a strictly conserved His as a heme ligand. TT1485 reconstituted with iron protoporphyrin IX chloride gave a low chlorite dismutase activity, indicating that TT1485 catalyzes a reaction other than chlorite degradation. The presence of a possible Fe–His–Asp triad in the heme proximal site suggests that TT1485 functions as a novel heme peroxidase to detoxify hydrogen peroxide within the cell.

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Abbreviations

MAD:

multiple wavelength anomalous dispersion

MLI:

muconolactone isomerase

SeMet:

selenomethionine

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Author notes

  1. Akihiro Okamoto

    Present address: Department of Biological Science and Technology, School of High-Technology for Human Welfare, Tokai University, Numazu, Shizuoka, 410-0395, Japan

Authors and Affiliations

  1. RIKEN Harima Institute at SPring-8, Kouto, Mikazuki-cho, Sayo-gun, Hyogo, 679-5148, Japan

    Akio Ebihara, Akihiro Okamoto, Yukihide Kousumi, Ryoji Masui, Shigeyuki Yokoyama & Seiki Kuramitsu

  2. Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka, 569-8686, Japan

    Akihiro Okamoto

  3. Departments of Chemistry, Osaka University, Toyonaka, Osaka, 560-0043, Japan

    Hitoshi Yamamoto & Norikazu Ueyama

  4. Departments of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan

    Ryoji Masui & Seiki Kuramitsu

  5. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

    Shigeyuki Yokoyama

  6. RIKEN Genomic Sciences Center, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan

    Shigeyuki Yokoyama & Seiki Kuramitsu

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  1. Akio Ebihara
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Correspondence to Seiki Kuramitsu.

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Ebihara, A., Okamoto, A., Kousumi, Y. et al. Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8. J Struct Funct Genomics 6, 21–32 (2005). https://doi.org/10.1007/s10969-005-1103-x

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  • DOI: https://doi.org/10.1007/s10969-005-1103-x

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