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PDBsum entry 1i2x
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DNA-RNA hybrid
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PDB id
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1i2x
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References listed in PDB file
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Key reference
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Title
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X-Ray crystallographic observation of "in-Line" and "adjacent" conformations in a bulged self-Cleaving RNA/DNA hybrid.
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Authors
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V.Tereshko,
S.T.Wallace,
N.Usman,
F.E.Wincott,
M.Egli.
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Ref.
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Rna, 2001,
7,
405-420.
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PubMed id
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Abstract
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The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo
self-cleavage at bulge sites in the presence of a variety of divalent metal ions
(Hüsken et al., Biochemistry, 1996, 35:16591-16600). Transesterification
proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide
attacking the 3'-adjacent phosphate group. The site-specificity of the reaction
is most likely a consequence of the greater local conformational freedom of the
RNA backbone in the bulge region. A standard A-form backbone geometry prohibits
formation of an in-line arrangement between 2'-oxygen and phosphate. However,
the backbone in the region of an unpaired nucleotide appears to be conducive to
an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction
represents one of the simplest RNA self-cleavage systems. Here we focus on the
conformational features of the RNA that underlie site-specific cleavage. The
structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed
in two crystal forms, permitting observation of 10 individual conformations of
the RNA bulge moiety. The bulge geometries cover a range of relative
arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond
(including adjacent and near in-line) and give a detailed picture of the
conformational changes necessary to line up the 2'-OH nucleophile and scissile
bond. Although metal ions are of crucial importance in the catalysis of
analogous cleavage reactions by ribozymes, it is clear that local strain or
conformational flexibility in the RNA also affect cleavage selectivity and rate
(Soukup & Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges
frozen out in the crystals provide snapshots along the reaction pathway prior to
the transition state of the phosphoryl transfer reaction.
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Headers
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