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PDBsum entry 1k2g
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References listed in PDB file
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Key reference
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Title
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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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Authors
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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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Ref.
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Rna, 2002,
8,
440-451.
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PubMed id
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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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Headers
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