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PDBsum entry 2a12
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Ribonucleic acid
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PDB id
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2a12
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References listed in PDB file
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Key reference
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Title
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A single active-Site region for a group ii intron.
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Authors
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A.De lencastre,
S.Hamill,
A.M.Pyle.
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Ref.
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Nat Struct Mol Biol, 2005,
12,
626-627.
[DOI no: ]
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PubMed id
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Abstract
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Despite the biological importance of self-splicing group II introns, little is
known about their structural organization. Synthetic incorporation of
site-specific photo-cross-linkers within catalytic domains resulted in
functional distance constraints that, when combined with known tertiary
interactions, provide a three-dimensional view of the active intron
architecture. All functionalities important for both steps of splicing are
proximal before the first step, suggestive of a single active-site region for
group II intron catalysis.
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Figure 1.
Figure 1. Photo-cross-links from the branch site and from the 3'
exon. (a) Polyacrylamide gel for visualization and isolation
of cross-linked [32P]D56 and [32P]D56(+1) species (bands A -C).
Lanes 1 and 2, unmodified D56; lanes 3 and 4, D56 containing a
s6dG at the branch site (A880); lanes 5 and 6, D56 ligated with
s6dG at the 3' end (D56(+1)). Cross-linking efficiencies are
3.3%, 5.1% and 1.2%, respectively, for bands A -C. (b) Mapping
of cross-links A and C by reverse transcriptase primer extension
(lanes 4 and 5, respectively; lane 3, primer extension control
on un-cross-linked material).
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Figure 2.
Figure 2. A close-up view of the active-site region, derived
from the ai5  gamma
group II intron model (Supplementary Fig. 4 online). Regions
of proximity are highlighted in green (G817, D5 bulge, first
nucleotides of the 5' exon and 3' exon, and the branch site
(A880)). The scissile phosphate (yellow ball), branch site 2'-OH
(red ball) and first nucleotide of the 3' exon (gray line) are
shown. Color scheme: IBS1, purple; 5'-end of domain 1, including
 ,
magenta; ',
pink; coordination loop-  ,
cyan; EBS1, brown; J2/3, blue; D5, red; bottom stem of D6,
orange.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2005,
12,
626-627)
copyright 2005.
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