Nucleic Acids Research, Vol 26, Issue 16 3717-3723, Copyright © 1998 by Oxford University Press
L Odell, V Huang, M Jakacka and T Pan
The ribozyme from bacterial ribonuclease P recognizes two structural
modules in a tRNA substrate: the T stem-loop and the acceptor stem. These
two modules are connected through a helical linker. The T stem- loop binds
at a surface confined in a folding domain away from the active site.
Substrates for the Bacillus subtilis RNase P RNA were previously selected
in vitro that are shown to bind comparably well or better than a tRNA
substrate. Chemical modification of P RNA-substrate complexes with
dimethylsulfate and kethoxal was performed to determine how the P RNA
recognizes three in vitro selected substrates. All three substrates bind at
the surface known to interact with the T stem-loop of tRNA. Similar to a
tRNA, the secondary structure of these substrates contains a helix around
the cleavage site and a hairpin loop at the corresponding position of the T
stem-loop. Unlike a tRNA, these two structural modules are connected
through a non-helical linker. The two structural modules in the tRNA and in
the selected substrates bind to two different domains in P RNA. The
properties of substrate recognition exhibited by this ribozyme may be
exploited to isolate new ribozyme- substrate pairs with interactive
structural modules.
ARTICLES
Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
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