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J. Biol. Chem., Vol. 276, Issue 30, 28380-28387, July 27, 2001
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From the Departments of Transcription factor Rho is a ring-shaped,
homohexameric protein that causes transcript termination through
actions on nascent RNAs that are coupled to ATP hydrolysis. The Rho
polypeptide has a distinct RNA binding domain of known structure as
well as an ATP binding domain for which a structure has been proposed
based on homology modeling. Treatment of Rho with
H2O2 in the presence of Fe-EDTA caused
single-cut cleavage at a number of points that coincide with
solvent-exposed loops in both the known and predicted structures,
thereby providing support for the validity of the tertiary and
quaternary structural models of Rho. The binding of ATP caused one
distinct change in the cleavage pattern, a strong protection at a
cleavage point in the P-loop of the ATP binding domain. Binding of RNA
and single-stranded DNA (poly(dC)) caused strong protection at several
accessible parts of the oligosaccharide/oligonucleotide binding (OB)
fold in the RNA binding domain. RNA molecules but not DNA molecules
also caused a strong, ATP-dependent protection at a cleavage site in
the predicted Q-loop of the ATP binding domain. These results suggest
that Rho has two distinct binding sites for RNA. Besides the site
composed of multiples of the RNA binding domain, to which
single-stranded DNA as well as RNA can bind, it has a separate,
RNA-specific site on the Q-loop in the ATP binding domain. In the
proposed quaternary structure of Rho, the Q-loops from the six subunits
form the upper entrance to the hole in the ring-shaped hexamer through
which the nascent transcript is translocated by actions coupled to ATP hydrolyses.
Identification of an RNA-binding Site in the ATP
Binding Domain of Escherichia coli Rho by
H2O2/Fe-EDTA Cleavage Protection Studies*
and Biology and
§ Chemistry Indiana University,
Bloomington, Indiana 47405
*
This research was supported by National Institutes of Health
Grant GM 56095.The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
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