PDBsum entry: 1rzw

Structural genomics, unknown function

PDB id: 1rzw

Contents

Protein chain

123 a.a. *

* Residue conservation analysis

PDB id:

1rzw

Name:

Structural genomics, unknown function

Title:

The solution structure of the archaeglobus fulgidis protein af2095. Northeast structural genomics consortium target gr4

Structure:

Protein af2095(gr4). Chain: a. Engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: af2095. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

1 models

Authors:

R.Powers,T.B.Acton,Y.J.Huang,J.Liu,L.Ma,B.Rost,Y.Chiang, J.R.Cort,M.A.Kennedy,G.T.Montelione,Northeast Structural Genomics Consortium (Nesg)

Key ref:

R.Powers et al. (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 Sci, 14, 2849-2861. PubMed id: 16251366 DOI: 10.1110/ps.051666705

Date:

29-Dec-03 Release date: 16-Nov-04

Protein chain

O28185  (PTH_ARCFU) -  Peptidyl-tRNA hydrolase

Seq: 115 a.a.

Struc: 123 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.1.29 - Aminoacyl-tRNA hydrolase.
• Reaction: N-substituted aminoacyl-tRNA + H₂O = N-substituted amino acid + tRNA

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: translation (1 term)
• Biochemical function: hydrolase activity (2 terms)

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.