Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes

Robert Powers, Nebojsa Mirkovic, Sharon Goldsmith-Fischman, Thomas B. Acton, Yiwen Chiang, Yuanpeng J. Huang, Lichung Ma, P. K. Rajan, John R. Cort, Michael A. Kennedy, Jinfeng Liu, Burkhard Rost, Barry Honig, Diana Murray, Gaetano T. Montelione

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Abstract

The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123-residue (13.6-kDa) protein, has been determined by NMR methods. The structure of AF2095 is comprised of four α-helices and a mixed β-sheet consisting of four parallel and anti-parallel β-strands, where the α-helices sandwich the β-sheet. Sequence and structural comparison of AF2095 with proteins from Homosapiens, Methanocaldococcus jannaschii, and Sulfolobus solfataricus reveals that AF2095 is a peptidyl-tRNA hydrolase (Pth2). This structural comparison also identifies putative catalytic residues and a tRNA interaction region for AF2095. The structure of AF2095 is also similar to the structure of protein TA0108 from archaea Thermoplasma acidophilum, which is deposited in the Protein Data Bank but not functionally annotated. The NMR structure of AF2095 has been further leveraged to obtain good-quality structural models for 55 other proteins. Although earlier studies have proposed that the Pth2 protein family is restricted to archeal and eukaryotic organisms, the similarity of the AF2095 structure to human Pth2, the conservation of key active-site residues, and the good quality of the resulting homology models demonstrate a large family of homologous Pth2 proteins that are conserved in eukaryotic, archaeal, and bacterial organisms, providing novel insights in the evolution of the Pth and Pth2 enzyme families.

Original languageEnglish (US)
Pages (from-to)2849-2861
Number of pages13
JournalProtein Science
Volume14
Issue number11
DOIs
StatePublished - Nov 1 2005

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Keywords

  • Archaeglobus fulgidis
  • NMR
  • Peptidyl-tRNA hydrolase Pth2
  • Protein AF2095
  • Pth2 evolution
  • Solution structure

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Powers, R., Mirkovic, N., Goldsmith-Fischman, S., Acton, T. B., Chiang, Y., Huang, Y. J., Ma, L., Rajan, P. K., Cort, J. R., Kennedy, M. A., Liu, J., Rost, B., Honig, B., Murray, D., & Montelione, G. T. (2005). Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes. Protein Science, 14(11), 2849-2861. https://doi.org/10.1110/ps.051666705