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* Residue conservation analysis
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PDB id:
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Ligase/RNA
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Title:
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Crystal structure of pyrococcus horikoshii arginyl-tRNA synthetase complexed with tRNA(arg)
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Structure:
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Arginyl-tRNA synthetase. Chain: a. Synonym: arginine--tRNA ligase, argrs. Engineered: yes. tRNA-arg. Chain: b. Engineered: yes
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Source:
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Pyrococcus horikoshii. Organism_taxid: 53953. Gene: args, ph1478. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: this tRNA occurs from pyrococcus horikoshii, in vitro transcription
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Resolution:
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2.30Å
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R-factor:
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0.201
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R-free:
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0.262
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Authors:
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M.Konno,T.Sumida,E.Uchikawa,Y.Mori,T.Yanagisawa,S.Sekine, S.Yokoyama
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Key ref:
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M.Konno
et al.
(2009).
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
Febs J,
276,
4763-4779.
PubMed id:
DOI:
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Date:
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16-Oct-08
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Release date:
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18-Aug-09
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PROCHECK
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Headers
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References
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O59147
(SYR_PYRHO) -
Arginyl-tRNA synthetase
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Seq:
Struc:
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629 a.a.
628 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.6.1.1.19
- Arginine--tRNA ligase.
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Reaction:
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ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)
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ATP
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+
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L-arginine
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+
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tRNA(Arg)
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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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L-arginyl-tRNA(Arg)
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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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3 terms
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Biochemical function
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nucleotide binding
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5 terms
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DOI no:
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Febs J
276:4763-4779
(2009)
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PubMed id:
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Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
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M.Konno,
T.Sumida,
E.Uchikawa,
Y.Mori,
T.Yanagisawa,
S.Sekine,
S.Yokoyama.
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ABSTRACT
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The ATP-pyrophosphate exchange reaction catalyzed by Arg-tRNA, Gln-tRNA and
Glu-tRNA synthetases requires the assistance of the cognate tRNA. tRNA also
assists Arg-tRNA synthetase in catalyzing the pyrophosphorolysis of synthetic
Arg-AMP at low pH. The mechanism by which the 3'-end A76, and in particular its
hydroxyl group, of the cognate tRNA is involved with the exchange reaction
catalyzed by those enzymes has yet to be established. We determined a crystal
structure of a complex of Arg-tRNA synthetase from Pyrococcus horikoshii,
tRNA(Arg)(CCU) and an ATP analog with Rfactor = 0.213 (Rfree = 0.253) at 2.0 A
resolution. On the basis of newly obtained structural information about the
position of ATP bound on the enzyme, we constructed a structural model for a
mechanism in which the formation of a hydrogen bond between the 2'-OH group of
A76 of tRNA and the carboxyl group of Arg induces both formation of Arg-AMP (Arg
+ ATP --> Arg-AMP + pyrophosphate) and pyrophosphorolysis of Arg-AMP (Arg-AMP
+ pyrophosphate --> Arg + ATP) at low pH. Furthermore, we obtained a
structural model of the molecular mechanism for the Arg-tRNA
synthetase-catalyzed deacylation of Arg-tRNA (Arg-tRNA + AMP --> Arg-AMP +
tRNA at high pH), in which the deacylation of aminoacyl-tRNA bound on Arg-tRNA
synthetase and Glu-tRNA synthetase is catalyzed by a quite similar mechanism,
whereby the proton-donating group (-NH-C+(NH2)2 or -COOH) of Arg and Glu assists
the aminoacyl transfer from the 2'-OH group of tRNA to the phosphate group of
AMP at high pH.
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