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PDBsum entry 1wnu
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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
102:11669-11674
(2005)
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PubMed id:
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Molecular basis of alanine discrimination in editing site.
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M.Sokabe,
A.Okada,
M.Yao,
T.Nakashima,
I.Tanaka.
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ABSTRACT
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AlaX is the homologue of the class II alanyl-tRNA synthetase editing domain and
has been shown to exhibit autonomous editing activity against mischarged
tRNA(Ala). Here, we present the structures of AlaX from the archaeon Pyrococcus
horikoshii in apo form, complexed with zinc, and with noncognate amino acid
l-serine and zinc. Together with mutational analysis, we demonstrated that the
conserved Thr-30 hydroxyl group located near the beta-methylene of the bound
serine is responsible for the discrimination of noncognate serine from cognate
alanine, based on their chemical natures. Furthermore, we confirmed that the
conserved Gln-584 in alanyl-tRNA synthetase, which corresponds to Thr-30 of
AlaX, is also critical for discrimination. These observations strongly suggested
conservation of the chemical discrimination among trans- and cis-editing of
tRNA(Ala).
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Selected figure(s)
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Figure 1.
Fig. 1. Domain organizations of AlaX, AlaRS, and ThrRS. The
boxes with hatched lines indicate the homologous editing
domains. The two vertical black stripes in the boxes show the
conserved HXXXH and CXXXH motifs.
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Figure 6.
Fig. 6. Recognition of tRNA moiety by AlaX. Shown is a
surface potential representation of PhoAlaX (A) and ThrRS-N2 (8)
(B), where acidic and basic potentials are represented in red
and blue, respectively. The serine and the SerA76 are shown as
stick models. The region corresponding to the hairpin motif is
circled with a green dashed line. (C) Superposition of PhoAlaX
(red tube) on ThrRS-N2–tRNA (yellow tube). (Left) The overview
of the superposed image. The third base pair is shown as a green
bar. (Right) An enlarged view of the hairpin motif interacting
with tRNA.
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Figures were
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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N.M.Reynolds,
B.A.Lazazzera,
and
M.Ibba
(2010).
Cellular mechanisms that control mistranslation.
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Nat Rev Microbiol,
8,
849-856.
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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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M.Guo,
Y.E.Chong,
K.Beebe,
R.Shapiro,
X.L.Yang,
and
P.Schimmel
(2009).
The C-Ala domain brings together editing and aminoacylation functions on one tRNA.
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Science,
325,
744-747.
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PDB code:
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M.Guo,
Y.E.Chong,
R.Shapiro,
K.Beebe,
X.L.Yang,
and
P.Schimmel
(2009).
Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma.
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Nature,
462,
808-812.
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PDB codes:
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M.Naganuma,
S.Sekine,
R.Fukunaga,
and
S.Yokoyama
(2009).
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
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Proc Natl Acad Sci U S A,
106,
8489-8494.
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PDB codes:
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M.Sokabe,
T.Ose,
A.Nakamura,
K.Tokunaga,
O.Nureki,
M.Yao,
and
I.Tanaka
(2009).
The structure of alanyl-tRNA synthetase with editing domain.
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Proc Natl Acad Sci U S A,
106,
11028-11033.
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PDB codes:
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T.K.Bhatt,
C.Kapil,
S.Khan,
M.A.Jairajpuri,
V.Sharma,
D.Santoni,
F.Silvestrini,
E.Pizzi,
and
A.Sharma
(2009).
A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum.
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BMC Genomics,
10,
644.
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K.Beebe,
M.Mock,
E.Merriman,
and
P.Schimmel
(2008).
Distinct domains of tRNA synthetase recognize the same base pair.
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Nature,
451,
90-93.
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Y.E.Chong,
X.L.Yang,
and
P.Schimmel
(2008).
Natural homolog of tRNA synthetase editing domain rescues conditional lethality caused by mistranslation.
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J Biol Chem,
283,
30073-30078.
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J.Ling,
H.Roy,
and
M.Ibba
(2007).
Mechanism of tRNA-dependent editing in translational quality control.
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Proc Natl Acad Sci U S A,
104,
72-77.
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R.Fukunaga,
and
S.Yokoyama
(2007).
Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii.
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Acta Crystallogr D Biol Crystallogr,
63,
390-400.
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PDB code:
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R.Fukunaga,
and
S.Yokoyama
(2007).
Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
224-228.
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J.Ishijima,
Y.Uchida,
C.Kuroishi,
C.Tuzuki,
N.Takahashi,
N.Okazaki,
K.Yutani,
and
M.Miyano
(2006).
Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution.
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Proteins,
62,
1133-1137.
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PDB code:
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J.W.Lee,
K.Beebe,
L.A.Nangle,
J.Jang,
C.M.Longo-Guess,
S.A.Cook,
M.T.Davisson,
J.P.Sundberg,
P.Schimmel,
and
S.L.Ackerman
(2006).
Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration.
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Nature,
443,
50-55.
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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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