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

¹ Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
² Department of Microbiology and Immunology, Institute for Computational Biomedicine, and Northeast Structural Genomics Consortium, Weill Medical College of Cornell University, New York, New York 10021, USA
³ Department of Biochemistry and Molecular Biophysics, and Northeast Structural Genomics Consortium, and ⁴ Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA
⁵ Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854, USA
⁶ Biological Sciences Division, and Northeast Structural Genomics Consortium, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
⁷ Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA

(RECEIVED June 21, 2005; FINAL REVISION August 4, 2005; ACCEPTED August 21, 2005)

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 -helices and a mixed -sheet consisting of four parallel and anti-parallel -strands, where the -helices sandwich the -sheet. Sequence and structural comparison of AF2095 with proteins from Homo sapiens, 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.

Keywords: NMR; Archaeglobus fulgidis; protein AF2095; solution structure; peptidyl-tRNA hydrolase Pth2; Pth2 evolution

Abbreviations: 3D, three dimensional • AES, N-terminal enhancer of split • Bit1, Bcl-2 inhibitor of transcription 1 • DTT, dithiothreitol • HNHA, amide proton to nitrogen to CH proton • HSQC, hetero-nuclear single quantum coherence spectroscopy • MES, 2-[N-morpholino]ethanesulfonic acid • NCBI, National Center for Biotechnology Information • NMR, nuclear magnetic resonance • NR, nonredundant NOE, nuclear Overhauser effect • NOESY, nuclear Overhauser enhancement spectroscopy • Pth, peptidyl tRNA hydrolase • PSSM, position-specific scoring matrix

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051666705.

Reprint requests to: Robert Powers, Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; e-mail: rpowers3{at}unl.edu; fax: (402) 472-2044.

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