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

  • Akio Ebihara
  • Akihiro Okamoto
  • Yukihide Kousumi
  • Hitoshi Yamamoto
  • Ryoji Masui
  • Norikazu Ueyama
  • Shigeyuki Yokoyama
  • Seiki Kuramitsu
Article

DOI: 10.1007/s10969-005-1103-x

Cite this article as:
Ebihara, A., Okamoto, A., Kousumi, Y. et al. J Struct Funct Genomics (2005) 6: 21. doi:10.1007/s10969-005-1103-x

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.

Keywords

chlorite dismutaseheme-binding proteinhypothetical proteinprotein evolutionstructure-based functional analysisstructural genomics

Abbreviations

MAD

multiple wavelength anomalous dispersion

MLI

muconolactone isomerase

SeMet

selenomethionine

Copyright information

© Springer 2005

Authors and Affiliations

  • Akio Ebihara
    • 1
  • Akihiro Okamoto
    • 1
    • 2
    • 7
  • Yukihide Kousumi
    • 1
  • Hitoshi Yamamoto
    • 3
  • Ryoji Masui
    • 1
    • 4
  • Norikazu Ueyama
    • 3
  • Shigeyuki Yokoyama
    • 1
    • 5
    • 6
  • Seiki Kuramitsu
    • 1
    • 4
    • 6
  1. 1.RIKEN Harima Institute at SPring-8Kouto, Mikazuki-cho, Sayo-gunJapan
  2. 2.Department of BiochemistryOsaka Medical CollegeTakatsukiJapan
  3. 3.Departments of ChemistryOsaka UniversityToyonakaJapan
  4. 4.Departments of Biology, Graduate School of ScienceOsaka UniversityToyonakaJapan
  5. 5.Department of Biophysics and Biochemistry, Graduate School of ScienceUniversity of TokyoHongo, Bunkyo-kuJapan
  6. 6.RIKEN Genomic Sciences CenterSuehiro-cho, TsurumiJapan
  7. 7.Department of Biological Science and Technology, School of High-Technology for Human WelfareTokai UniversityNumazuJapan