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Structural genomics, unknown function
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PDB id
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1rzw
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Contents |
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* Residue conservation analysis
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PDB id:
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Structural genomics, unknown function
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Title:
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The solution structure of the archaeglobus fulgidis protein af2095. Northeast structural genomics consortium target gr4
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Structure:
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Protein af2095(gr4). Chain: a. Engineered: yes
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Source:
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Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: af2095. Expressed in: escherichia coli. Expression_system_taxid: 562.
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NMR struc:
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1 models
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Authors:
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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)
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Key ref:
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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:
DOI:
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Date:
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29-Dec-03
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Release date:
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16-Nov-04
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PROCHECK
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Headers
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References
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O28185
(PTH_ARCFU) -
Peptidyl-tRNA hydrolase
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Seq: Struc:
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115 a.a.
123 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.3.1.1.29
- Aminoacyl-tRNA hydrolase.
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Reaction:
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N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
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N-substituted aminoacyl-tRNA
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+
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H(2)O
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=
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N-substituted amino acid
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+
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tRNA
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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cytoplasm
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1 term
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Biological process
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translation
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1 term
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Biochemical function
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hydrolase activity
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2 terms
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DOI no:
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Protein Sci
14:2849-2861
(2005)
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PubMed id:
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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.
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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.
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ABSTRACT
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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.
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Selected figure(s)
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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]
).
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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.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2005,
14,
2849-2861)
copyright 2005.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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R.Szklarczyk,
and
M.A.Huynen
(2010).
Mosaic origin of the mitochondrial proteome.
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Proteomics, 10,
4012-4024.
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S.Halouska,
Y.Zhou,
D.F.Becker,
and
R.Powers
(2009).
Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex.
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Proteins, 75,
12-27.
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PDB codes:
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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.
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Acta Crystallogr D Biol Crystallogr, 64,
444-453.
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PDB codes:
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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.
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Biol Chem, 388,
467-479.
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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.
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Proteins, 66,
766-777.
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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.
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Proteins, 65,
124-135.
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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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