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PDBsum entry 1htt
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Complex (tRNA synthetase/his-adenylate)
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PDB id
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1htt
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Complex (tRNA synthetase/his-adenylate)
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Title:
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Histidyl-tRNA synthetase
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Structure:
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Histidyl-tRNA synthetase. Chain: a, b, c, d. Synonym: histidine-tRNA ligase. Engineered: yes
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Source:
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Escherichia coli. Organism_taxid: 562. Strain: jm109. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Tetramer (from
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Resolution:
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2.60Å
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R-factor:
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0.246
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R-free:
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0.327
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Authors:
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J.G.Arnez,D.C.Harris,A.Mitschler,B.Rees,C.S.Francklyn,D.Moras
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Key ref:
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J.G.Arnez
et al.
(1995).
Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate.
Embo J,
14,
4143-4155.
PubMed id:
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Date:
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09-Mar-96
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Release date:
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27-Jan-97
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PROCHECK
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Headers
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References
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P60906
(SYH_ECOLI) -
Histidine--tRNA ligase from Escherichia coli (strain K12)
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Seq:
Struc:
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424 a.a.
366 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.6.1.1.21
- histidine--tRNA ligase.
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Reaction:
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tRNA(His) + L-histidine + ATP = L-histidyl-tRNA(His) + AMP + diphosphate + H+
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tRNA(His)
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+
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L-histidine
Bound ligand (Het Group name = )
matches with 90.91% similarity
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+
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ATP
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=
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L-histidyl-tRNA(His)
Bound ligand (Het Group name = )
corresponds exactly
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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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Embo J
14:4143-4155
(1995)
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PubMed id:
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Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate.
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J.G.Arnez,
D.C.Harris,
A.Mitschler,
B.Rees,
C.S.Francklyn,
D.Moras.
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ABSTRACT
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The crystal structure at 2.6 A of the histidyl-tRNA synthetase from Escherichia
coli complexed with histidyl-adenylate has been determined. The enzyme is a
homodimer with a molecular weight of 94 kDa and belongs to the class II of
aminoacyl-tRNA synthetases (aaRS). The asymmetric unit is composed of two
homodimers. Each monomer consists of two domains. The N-terminal catalytic core
domain contains a six-stranded antiparallel beta-sheet sitting on two
alpha-helices, which can be superposed with the catalytic domains of yeast
AspRS, and GlyRS and SerRS from Thermus thermophilus with a root-mean-square
difference on the C alpha atoms of 1.7-1.9 A. The active sites of all four
monomers are occupied by histidyl-adenylate, which apparently forms during
crystallization. The 100 residue C-terminal alpha/beta domain resembles half of
a beta-barrel, and provides an independent domain oriented to contact the
anticodon stem and part of the anticodon loop of tRNA(His). The modular domain
organization of histidyl-tRNA synthetase reiterates a repeated theme in aaRS,
and its structure should provide insight into the ability of certain aaRS to
aminoacylate minihelices and other non-tRNA molecules.
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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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S.B.Pierce,
K.M.Chisholm,
E.D.Lynch,
M.K.Lee,
T.Walsh,
J.M.Opitz,
W.Li,
R.E.Klevit,
and
M.C.King
(2011).
Mutations in mitochondrial histidyl tRNA synthetase HARS2 cause ovarian dysgenesis and sensorineural hearing loss of Perrault syndrome.
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Proc Natl Acad Sci U S A,
108,
6543-6548.
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E.A.Merritt,
T.L.Arakaki,
J.R.Gillespie,
E.T.Larson,
A.Kelley,
N.Mueller,
A.J.Napuli,
J.Kim,
L.Zhang,
C.L.Verlinde,
E.Fan,
F.Zucker,
F.S.Buckner,
W.C.van Voorhis,
and
W.G.Hol
(2010).
Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs.
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J Mol Biol,
397,
481-494.
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PDB codes:
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S.Shaul,
D.Berel,
Y.Benjamini,
and
D.Graur
(2010).
Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications.
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RNA,
16,
141-153.
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B.Kimura,
H.Takahashi,
S.Hokimoto,
Y.Tanaka,
and
T.Fujii
(2009).
Induction of the histidine decarboxylase genes of Photobacterium damselae subsp. damselae (formally P. histaminum) at low pH.
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J Appl Microbiol,
107,
485-497.
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E.Guth,
M.Farris,
M.Bovee,
and
C.S.Francklyn
(2009).
Asymmetric amino acid activation by class II histidyl-tRNA synthetase from Escherichia coli.
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J Biol Chem,
284,
20753-20762.
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G.Sharma,
and
E.A.First
(2009).
Thermodynamic Analysis Reveals a Temperature-dependent Change in the Catalytic Mechanism of Bacillus stearothermophilus Tyrosyl-tRNA Synthetase.
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J Biol Chem,
284,
4179-4190.
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S.M.Levine,
N.Raben,
D.Xie,
F.B.Askin,
R.Tuder,
M.Mullins,
A.Rosen,
and
L.A.Casciola-Rosen
(2007).
Novel conformation of histidyl-transfer RNA synthetase in the lung: the target tissue in Jo-1 autoantibody-associated myositis.
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Arthritis Rheum,
56,
2729-2739.
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A.G.Hinnebusch
(2005).
Translational regulation of GCN4 and the general amino acid control of yeast.
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Annu Rev Microbiol,
59,
407-450.
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A.K.Padyana,
H.Qiu,
A.Roll-Mecak,
A.G.Hinnebusch,
and
S.K.Burley
(2005).
Structural basis for autoinhibition and mutational activation of eukaryotic initiation factor 2alpha protein kinase GCN2.
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J Biol Chem,
280,
29289-29299.
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PDB codes:
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K.S.Champagne,
M.Sissler,
Y.Larrabee,
S.Doublié,
and
C.S.Francklyn
(2005).
Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog.
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J Biol Chem,
280,
34096-34104.
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PDB codes:
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M.L.Bovee,
M.A.Pierce,
and
C.S.Francklyn
(2003).
Induced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase.
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Biochemistry,
42,
15102-15113.
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M.Seetharaman,
C.Williams,
C.J.Cramer,
and
K.Musier-Forsyth
(2003).
Effect of G-1 on histidine tRNA microhelix conformation.
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Nucleic Acids Res,
31,
7311-7321.
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H.Qiu,
J.Dong,
C.Hu,
C.S.Francklyn,
and
A.G.Hinnebusch
(2001).
The tRNA-binding moiety in GCN2 contains a dimerization domain that interacts with the kinase domain and is required for tRNA binding and kinase activation.
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EMBO J,
20,
1425-1438.
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R.Fishman,
V.Ankilova,
N.Moor,
and
M.Safro
(2001).
Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese.
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Acta Crystallogr D Biol Crystallogr,
57,
1534-1544.
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PDB code:
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S.A.Hawko,
and
C.S.Francklyn
(2001).
Covariation of a specificity-determining structural motif in an aminoacyl-tRNA synthetase and a tRNA identity element.
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Biochemistry,
40,
1930-1936.
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A.K.Forrest,
R.L.Jarvest,
L.M.Mensah,
P.J.O'Hanlon,
A.J.Pope,
and
R.J.Sheppard
(2000).
Aminoalkyl adenylate and aminoacyl sulfamate intermediate analogues differing greatly in affinity for their cognate Staphylococcus aureus aminoacyl tRNA synthetases.
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Bioorg Med Chem Lett,
10,
1871-1874.
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A.Yaremchuk,
S.Cusack,
and
M.Tukalo
(2000).
Crystal structure of a eukaryote/archaeon-like protyl-tRNA synthetase and its complex with tRNAPro(CGG).
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EMBO J,
19,
4745-4758.
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I.Sugiura,
O.Nureki,
Y.Ugaji-Yoshikawa,
S.Kuwabara,
A.Shimada,
M.Tateno,
B.Lorber,
R.Giegé,
D.Moras,
S.Yokoyama,
and
M.Konno
(2000).
The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules.
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Structure,
8,
197-208.
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PDB code:
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J.Dong,
H.Qiu,
M.Garcia-Barrio,
J.Anderson,
and
A.G.Hinnebusch
(2000).
Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain.
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Mol Cell,
6,
269-279.
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K.A.Denessiouk,
and
M.S.Johnson
(2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
|
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Proteins,
38,
310-326.
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M.Ibba,
and
D.Soll
(2000).
Aminoacyl-tRNA synthesis.
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Annu Rev Biochem,
69,
617-650.
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M.Kaminska,
M.Deniziak,
P.Kerjan,
J.Barciszewski,
and
M.Mirande
(2000).
A recurrent general RNA binding domain appended to plant methionyl-tRNA synthetase acts as a cis-acting cofactor for aminoacylation.
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EMBO J,
19,
6908-6917.
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R.Sood,
A.C.Porter,
D.A.Olsen,
D.R.Cavener,
and
R.C.Wek
(2000).
A mammalian homologue of GCN2 protein kinase important for translational control by phosphorylation of eukaryotic initiation factor-2alpha.
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Genetics,
154,
787-801.
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V.Cura,
D.Moras,
and
D.Kern
(2000).
Sequence analysis and modular organization of threonyl-tRNA synthetase from Thermus thermophilus and its interrelation with threonyl-tRNA synthetases of other origins.
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Eur J Biochem,
267,
379-393.
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V.Guez,
S.Nair,
A.Chaffotte,
and
H.Bedouelle
(2000).
The anticodon-binding domain of tyrosyl-tRNA synthetase: state of folding and origin of the crystallographic disorder.
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Biochemistry,
39,
1739-1747.
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A.J.Morales,
M.A.Swairjo,
and
P.Schimmel
(1999).
Structure-specific tRNA-binding protein from the extreme thermophile Aquifex aeolicus.
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EMBO J,
18,
3475-3483.
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M.Sissler,
C.Delorme,
J.Bond,
S.D.Ehrlich,
P.Renault,
and
C.Francklyn
(1999).
An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis.
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Proc Natl Acad Sci U S A,
96,
8985-8990.
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W.Freist,
J.F.Verhey,
A.Rühlmann,
D.H.Gauss,
and
J.G.Arnez
(1999).
Histidyl-tRNA synthetase.
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Biol Chem,
380,
623-646.
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B.Felden,
and
R.Giegé
(1998).
Resected RNA pseudoknots and their recognition by histidyl-tRNA synthetase.
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Proc Natl Acad Sci U S A,
95,
10431-10436.
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C.Briand,
A.Poterszman,
A.Mitschler,
M.Yusupov,
J.C.Thierry,
and
D.Moras
(1998).
Crystals of Thermus thermophilus tRNAAsp complexed with its cognate aspartyl-tRNA synthetase have a solvent content of 75%. Comparison with other aminoacylation systems.
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Acta Crystallogr D Biol Crystallogr,
54,
1382-1386.
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D.S.Olsen,
B.Jordan,
D.Chen,
R.C.Wek,
and
D.R.Cavener
(1998).
Isolation of the gene encoding the Drosophila melanogaster homolog of the Saccharomyces cerevisiae GCN2 eIF-2alpha kinase.
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Genetics,
149,
1495-1509.
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E.Sattlegger,
A.G.Hinnebusch,
and
I.B.Barthelmess
(1998).
cpc-3, the Neurospora crassa homologue of yeast GCN2, encodes a polypeptide with juxtaposed eIF2alpha kinase and histidyl-tRNA synthetase-related domains required for general amino acid control.
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J Biol Chem,
273,
20404-20416.
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J.Cavarelli,
B.Delagoutte,
G.Eriani,
J.Gangloff,
and
D.Moras
(1998).
L-arginine recognition by yeast arginyl-tRNA synthetase.
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EMBO J,
17,
5438-5448.
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PDB code:
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L.Ribas de Pouplana,
D.Buechter,
N.Y.Sardesai,
and
P.Schimmel
(1998).
Functional analysis of peptide motif for RNA microhelix binding suggests new family of RNA-binding domains.
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EMBO J,
17,
5449-5457.
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R.Brouwer,
W.Vree Egberts,
P.H.Jongen,
B.G.van Engelen,
and
W.J.van Venrooij
(1998).
Frequent occurrence of anti-tRNA(His) autoantibodies that recognize a conformational epitope in sera of patients with myositis.
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Arthritis Rheum,
41,
1428-1437.
|
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S.Cusack,
A.Yaremchuk,
I.Krikliviy,
and
M.Tukalo
(1998).
tRNA(Pro) anticodon recognition by Thermus thermophilus prolyl-tRNA synthetase.
|
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Structure,
6,
101-108.
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T.Nakatsu,
H.Kato,
and
J.Oda
(1998).
Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.
|
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Nat Struct Biol,
5,
15-19.
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PDB codes:
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V.L.Rath,
L.F.Silvian,
B.Beijer,
B.S.Sproat,
and
T.A.Steitz
(1998).
How glutaminyl-tRNA synthetase selects glutamine.
|
| |
Structure,
6,
439-449.
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PDB code:
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A.Aberg,
A.Yaremchuk,
M.Tukalo,
B.Rasmussen,
and
S.Cusack
(1997).
Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase.
|
| |
Biochemistry,
36,
3084-3094.
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PDB codes:
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B.F.Clark,
and
J.Nyborg
(1997).
The ternary complex of EF-Tu and its role in protein biosynthesis.
|
| |
Curr Opin Struct Biol,
7,
110-116.
|
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C.Stehlin,
D.H.Heacock,
H.Liu,
and
K.Musier-Forsyth
(1997).
Chemical modification and site-directed mutagenesis of the single cysteine in motif 3 of class II Escherichia coli prolyl-tRNA synthetase.
|
| |
Biochemistry,
36,
2932-2938.
|
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|
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|
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J.Augustine,
and
C.Francklyn
(1997).
Design of an active fragment of a class II aminoacyl-tRNA synthetase and its significance for synthetase evolution.
|
| |
Biochemistry,
36,
3473-3482.
|
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|
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J.G.Arnez,
J.G.Augustine,
D.Moras,
and
C.S.Francklyn
(1997).
The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase.
|
| |
Proc Natl Acad Sci U S A,
94,
7144-7149.
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PDB codes:
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J.Rudinger,
B.Felden,
C.Florentz,
and
R.Giegé
(1997).
Strategy for RNA recognition by yeast histidyl-tRNA synthetase.
|
| |
Bioorg Med Chem,
5,
1001-1009.
|
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S.Cusack
(1997).
Aminoacyl-tRNA synthetases.
|
| |
Curr Opin Struct Biol,
7,
881-889.
|
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F.Agou,
J.P.Waller,
and
M.Mirande
(1996).
Expression of rat aspartyl-tRNA synthetase in Saccharomyces cerevisiae. Role of the NH2-terminal polypeptide extension on enzyme activity and stability.
|
| |
J Biol Chem,
271,
29295-29303.
|
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P.Romby,
J.Caillet,
C.Ebel,
C.Sacerdot,
M.Graffe,
F.Eyermann,
C.Brunel,
H.Moine,
C.Ehresmann,
B.Ehresmann,
and
M.Springer
(1996).
The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions.
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| |
EMBO J,
15,
5976-5987.
|
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|
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R.K.Airas
(1996).
Differences in the magnesium dependences of the class I and class II aminoacyl-tRNA synthetases from Escherichia coli.
|
| |
Eur J Biochem,
240,
223-231.
|
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S.Brenner,
and
L.M.Corrochano
(1996).
Translocation events in the evolution of aminoacyl-tRNA synthetases.
|
| |
Proc Natl Acad Sci U S A,
93,
8485-8489.
|
|
|
|
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|
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S.Gillet,
C.B.Hoang,
J.M.Schmitter,
T.Fukui,
S.Blanquet,
and
C.Hountondji
(1996).
Affinity labeling of Escherichia coli histidyl-tRNA synthetase with reactive ATP analogues. Identification of labeled amino acid residues by matrix assisted laser desorption-ionization mass spectrometry.
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Eur J Biochem,
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S.P.Hale,
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(1996).
Protein synthesis editing by a DNA aptamer.
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Proc Natl Acad Sci U S A,
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S.Zhu,
A.Y.Sobolev,
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(1996).
Histidyl-tRNA synthetase-related sequences in GCN2 protein kinase regulate in vitro phosphorylation of eIF-2.
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J Biol Chem,
271,
24989-24994.
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D.T.Logan,
M.H.Mazauric,
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(1995).
Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus.
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EMBO J,
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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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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