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PDBsum entry 3bbk
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References listed in PDB file
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Key reference
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Title
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Structural effects of nucleobase variations at key active site residue ade38 in the hairpin ribozyme.
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Authors
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C.Macelrevey,
J.D.Salter,
J.Krucinska,
J.E.Wedekind.
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Ref.
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Rna, 2008,
14,
1600-1616.
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PubMed id
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Abstract
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The hairpin ribozyme requires functional groups from Ade38 to achieve efficient
bond cleavage or ligation. To identify molecular features that contribute to
catalysis, structures of position 38 base variants 2,6-diaminopurine (DAP),
2-aminopurine (AP), cytosine (Cyt), and guanine (Gua) were determined between
2.2 and 2.8 A resolution. For each variant, two substrate modifications were
compared: (1) a 2'-O-methyl-substituent at Ade-1 was used in lieu of the
nucleophile to mimic the precatalytic state, and (2) a
3'-deoxy-2',5'-phosphodiester linkage between Ade-1 and Gua+1 was used to mimic
a reaction-intermediate conformation. While the global fold of each variant
remained intact, the results revealed the importance of Ade38 N1 and N6 groups.
Absence of N6 resulting from AP38 coincided with failure to localize the
precatalytic scissile phosphate. Cyt38 severely impaired catalysis in a prior
study, and its structures here indicated an anti base conformation that
sequesters the imino moiety from the scissile bond. Gua38 was shown to be even
more deleterious to activity. Although the precatalytic structure was nominally
affected, the reaction-intermediate conformation indicated a severe
electrostatic clash between the Gua38 keto oxygen and the pro-Rp oxygen of the
scissile bond. Overall, position 38 modifications solved in the presence of
2'-OMe Ade-1 deviated from in-line geometry, whereas variants with a 2',5'
linkage exhibited S-turn destabilization, as well as base conformational changes
from syn to anti. These findings demonstrate the importance of the Ade38
Watson-Crick face in attaining a reaction-intermediate state and the sensitivity
of the RNA fold to restructuring when electrostatic and shape features fail to
complement.
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Headers
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