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PDBsum entry 2amc
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Contents |
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* Residue conservation analysis
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Enzyme class:
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Chains A, B:
E.C.6.1.1.20
- phenylalanine--tRNA ligase.
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Reaction:
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tRNA(Phe) + L-phenylalanine + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H+
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tRNA(Phe)
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+
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L-phenylalanine
Bound ligand (Het Group name = )
matches with 92.31% similarity
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+
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ATP
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=
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L-phenylalanyl-tRNA(Phe)
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+
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AMP
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+
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diphosphate
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Structure
13:1799-1807
(2005)
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PubMed id:
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Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase.
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O.Kotik-Kogan,
N.Moor,
D.Tworowski,
M.Safro.
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ABSTRACT
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Aminoacyl-tRNA synthetases (aaRSs) exert control over the faithful transfer of
amino acids onto cognate tRNAs. Since chemical structures of various amino acids
closely resemble each other, it is difficult to discriminate between them.
Editing activity has been evolved by certain aaRSs to resolve the problem. In
this study, we determined the crystal structures of complexes of T. thermophilus
phenylalanyl-tRNA synthetase (PheRS) with L-tyrosine, p-chloro-phenylalanine,
and a nonhydrolyzable tyrosyl-adenylate analog. The structures demonstrate
plasticity of the synthetic site capable of binding substrates larger than
phenylalanine and provide a structural basis for the proofreading mechanism. The
editing site is localized at the B3/B4 interface, 35 A from the synthetic site.
Glubeta334 plays a crucial role in the specific recognition of the Tyr moiety in
the editing site. The tyrosyl-adenylate analog binds exclusively in the
synthetic site. Both structural data and tyrosine-dependent ATP hydrolysis
enhanced by tRNA(Phe) provide evidence for a preferential posttransfer editing
pathway in the phenylalanine-specific system.
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Selected figure(s)
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Figure 3.
Figure 3. View of the Editing Site of T. thermophilus PheRS
Showing the Interactions with L-Tyrosine
(A) PheRS editing
site (colored green) with bound Tyr (colored orange). The
electron density map is contoured at 2.5s. The protein residues
participating in direct and water-mediated (red spheres)
contacts are shown.
(B) Schematic drawing of the
interactions with Tyr. Direct and water (marked as S)-mediated H
bonds are shown by dashed lines. Van der Waals interactions are
depicted by solid arrows.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2005,
13,
1799-1807)
copyright 2005.
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Figure was
selected
by an automated process.
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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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I.Mermershtain,
I.Finarov,
L.Klipcan,
N.Kessler,
H.Rozenberg,
and
M.G.Safro
(2011).
Idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP.
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Protein Sci,
20,
160-167.
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PDB code:
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I.Finarov,
N.Moor,
N.Kessler,
L.Klipcan,
and
M.G.Safro
(2010).
Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns.
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Structure,
18,
343-353.
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PDB code:
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O.Khersonsky,
and
D.S.Tawfik
(2010).
Enzyme promiscuity: a mechanistic and evolutionary perspective.
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Annu Rev Biochem,
79,
471-505.
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B.R.Villiers,
and
F.Hollfelder
(2009).
Mapping the limits of substrate specificity of the adenylation domain of TycA.
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Chembiochem,
10,
671-682.
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J.Ling,
B.R.So,
S.S.Yadavalli,
H.Roy,
S.Shoji,
K.Fredrick,
K.Musier-Forsyth,
and
M.Ibba
(2009).
Resampling and editing of mischarged tRNA prior to translation elongation.
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Mol Cell,
33,
654-660.
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J.Ling,
N.Reynolds,
and
M.Ibba
(2009).
Aminoacyl-tRNA synthesis and translational quality control.
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Annu Rev Microbiol,
63,
61-78.
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L.Klipcan,
I.Levin,
N.Kessler,
N.Moor,
I.Finarov,
and
M.Safro
(2008).
The tRNA-induced conformational activation of human mitochondrial phenylalanyl-tRNA synthetase.
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Structure,
16,
1095-1104.
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PDB code:
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B.Zhu,
M.W.Zhao,
G.Eriani,
and
E.D.Wang
(2007).
A present-day aminoacyl-tRNA synthetase with ancestral editing properties.
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RNA,
13,
15-21.
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I.Levin,
N.Kessler,
N.Moor,
L.Klipcan,
E.Koc,
P.Templeton,
L.Spremulli,
and
M.Safro
(2007).
Purification, crystallization and preliminary X-ray characterization of a human mitochondrial phenylalanyl-tRNA synthetase.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
761-764.
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T.Crepin,
A.Yaremchuk,
M.Tukalo,
and
S.Cusack
(2006).
Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.
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Structure,
14,
1511-1525.
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PDB codes:
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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
code is
shown on the right.
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Links
