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PDBsum entry 1k2g
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PDB id:
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RNA
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Title:
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Structural basis for the 3'-terminal guanosine recognition by the group i intron
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Structure:
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5'-r( Cp Ap Gp Ap Cp Up Up Cp Gp Gp Up Cp Gp Cp Ap Gp Ap Gp Ap Up Gp G)-3'. Chain: a. Engineered: yes. Other_details: p7-p9.0 domain of RNA group i intron
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Source:
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Synthetic: yes. Other_details: sequence from tetrahymena thermophila.
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NMR struc:
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1 models
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Authors:
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Y.Kitamura,Y.Muto,S.Watanabe,I.Kim,T.Ito,Y.Nishiya,K.Sakamoto, T.Ohtsuki,G.Kawai,K.Watanabe,K.Hosono,H.Takaku,E.Katoh,T.Yamazaki, T.Inoue,S.Yokoyama
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Key ref:
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A.Kitamura
et al.
(2002).
Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.
Rna,
8,
440-451.
PubMed id:
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Date:
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27-Sep-01
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Release date:
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08-May-02
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Headers
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References
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C-A-G-A-C-U-U-C-G-G-U-C-G-C-A-G-A-G-A-U-G-G
22 bases
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Rna
8:440-451
(2002)
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PubMed id:
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Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.
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A.Kitamura,
Y.Muto,
S.Watanabe,
I.Kim,
T.Ito,
Y.Nishiya,
K.Sakamoto,
T.Ohtsuki,
G.Kawai,
K.Watanabe,
K.Hosono,
H.Takaku,
E.Katoh,
T.Yamazaki,
T.Inoue,
S.Yokoyama.
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ABSTRACT
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In the second step of the two consecutive transesterifications of the
self-splicing reaction of the group I intron, the conserved guanosine at the 3'
terminus of the intron (omegaG) binds to the guanosine-binding site (GBS) in the
intron. In the present study, we designed a 22-nt model RNA (GBS/omegaG)
including the GBS and omegaG from the Tetrahymena group I intron, and determined
the solution structure by NMR methods. In this structure, omegaG is recognized
by the formation of a base triple with the G264 x C311 base pair, and this
recognition is stabilized by the stacking interaction between omegaG and C262.
The bulged structure at A263 causes a large helical twist angle (40 +/- 80)
between the G264 x C311 and C262 x G312 base pairs. We named this type of
binding pocket with a bulge and a large twist, formed on the major groove, a
"Bulge-and-Twist" (BT) pocket. With another twist angle between the C262 x G312
and G413 x C313 base pairs (45 +/- 100), the axis of GBS/omegaG is kinked at the
GBS region. This kinked axis superimposes well on that of the corresponding
region in the structure model built on a 5.0 A resolution electron density map
(Golden et al., Science, 1998, 282:345-358). This compact structure of the GBS
is also consistent with previous biochemical studies on group I introns. The BT
pockets are also found in the arginine-binding site of the HIV-TAR RNA, and
within the 16S rRNA and the 23S rRNA.
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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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A.Kitamura,
P.J.Jardine,
D.L.Anderson,
S.Grimes,
and
H.Matsuo
(2008).
Analysis of intermolecular base pair formation of prohead RNA of the phage phi29 DNA packaging motor using NMR spectroscopy.
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Nucleic Acids Res,
36,
839-848.
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J.M.Carothers,
J.H.Davis,
J.J.Chou,
and
J.W.Szostak
(2006).
Solution structure of an informationally complex high-affinity RNA aptamer to GTP.
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RNA,
12,
567-579.
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PDB code:
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P.L.Adams,
M.R.Stahley,
M.L.Gill,
A.B.Kosek,
J.Wang,
and
S.A.Strobel
(2004).
Crystal structure of a group I intron splicing intermediate.
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RNA,
10,
1867-1887.
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H.Nielsen,
T.Fiskaa,
A.B.Birgisdottir,
P.Haugen,
C.Einvik,
and
S.Johansen
(2003).
The ability to form full-length intron RNA circles is a general property of nuclear group I introns.
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RNA,
9,
1464-1475.
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S.Kurata,
T.Ohtsuki,
T.Suzuki,
and
K.Watanabe
(2003).
Quick two-step RNA ligation employing periodate oxidation.
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Nucleic Acids Res,
31,
e145.
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M.I.Newby,
and
N.L.Greenbaum
(2002).
Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine.
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Nat Struct Biol,
9,
958-965.
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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
