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PDBsum entry 1afx
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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 the loop b domain from the hairpin ribozyme.
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Authors
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S.E.Butcher,
F.H.Allain,
J.Feigon.
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Ref.
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Nat Struct Biol, 1999,
6,
212-216.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
0%.
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Abstract
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The hairpin ribozyme is a small catalytic RNA with a unique two-domain
structure. Here we present the solution structure of the loop B domain of the
hairpin ribozyme, which contains most of the catalytically essential
nucleotides. The 38-nucleotide domain contains a 16-nucleotide internal loop
that forms one of the largest non-Watson-Crick segments of base pairing thus far
determined by either NMR or crystallography. Since the solution structure of the
smaller loop A domain has been previously solved, an NMR structure-based model
of the 22,000 Mr hairpin ribozyme-substrate open complex emerges by joining the
two domain structures. Strikingly, catalytically essential functional groups for
the loop B domain are concentrated within an expanded minor groove, presenting a
clear docking surface for the loop A domain.
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Figure 2.
Figure 2. The 10 lowest energy structures (of 28 converged
structures; Table 1). a, Structures superimposed on the
internal loop B (residues 20−26, 36−40, 42−44). View is
into the minor groove of the internal loop B. Stem 1 and stem 2
and UUCG tetraloop from the lowest energy structure are shown.
b, Superimposition on the residues forming the UV-photosensitive
module (residues 20−23, 40−44). c, Superimposition on the 12
residues forming the lower stem and the UUCG tetraloop. Adenine
nucleotides are shown in red, guanines in green, cytosines in
yellow and uracils in cyan. For clarity, only 10 structures are
shown superimposed.
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Figure 3.
Figure 3. a, Stereo view of the lowest energy structure of the
internal loop B. b, The seven non-Watson−Crick base pairs
of the lowest energy structure. These base orientations were
found for the majority of the 28 converged structures of loop B.
Color scheme is the same as Fig. 2.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(1999,
6,
212-216)
copyright 1999.
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Headers
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