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123 a.a.
 N-substituted aminoacyl-tRNA |
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H(2)O |
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 N-substituted amino acid |
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Key reference
DOI no: 10.1110/ps.051666705 Protein Sci 14:2849-2861 (2005) PubMed id: 16251366
Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes. R.Powers, N.Mirkovic, S.Goldsmith-Fischman, T.B.Acton, Y.Chiang, Y.J.Huang, L.Ma, P.K.Rajan, J.R.Cort, M.A.Kennedy, J.Liu, B.Rost, B.Honig, D.Murray, G.T.Montelione. 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 alpha-helices and a mixed beta-sheet consisting of four parallel and anti-parallel beta-strands, where the alpha-helices sandwich the beta-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.
Selected figure(s)
Figure 3.
Figure 3. Ribbon diagrams of the aligned views of (A) human Pth2 (PDB ID 1q7s [PDB] ), (B) T. acidophilum TA0108 (PDB ID 1rlk [PDB] ), and (C) A. fulgidis AF2095 (GR4; PDB ID 1rzw [PDB] ).Figure 4.
Figure 4. Phylogenic tree of Pth2 enzymes with <30% sequence similarity to AF2095, including homologs. For clarity, each major branch is colored separately, each organism is labeled archaea (A), eukaryote (E), and eubacteria (Eu), and the homologs are numbered sequentially.
The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 2849-2861) copyright 2005. Figures were selected by the author.
Literature references that cite this PDB file's key reference
PubMed id Reference
18767154 S.Halouska, Y.Zhou, D.F.Becker, and R.Powers (2009).
Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex.Proteins, 75, 12-27.
PDB codes: 2jxg 2jxh 2jxi
18391411 K.Shimizu, C.Kuroishi, M.Sugahara, and N.Kunishima (2008).
Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state.Acta Crystallogr D Biol Crystallogr, 64, 444-453.
PDB codes: 1wn2 2d3k
17516842 N.C.Bal, H.Agrawal, A.K.Meher, and A.Arora (2007).
Characterization of peptidyl-tRNA hydrolase encoded by open reading frame Rv1014c of Mycobacterium tuberculosis H37Rv.Biol Chem, 388, 467-479.
17154423 N.Mirkovic, Z.Li, A.Parnassa, and D.Murray (2007).
Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization.Proteins, 66, 766-777.
16862592 R.Powers, J.C.Copeland, K.Germer, K.A.Mercier, V.Ramanathan, and P.Revesz (2006).
Comparison of protein active site structures for functional annotation of proteins and drug design.Proteins, 65, 124-135. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.
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