RNA Remodeling Enzymes
RNA metabolism requires that RNA folding be coordinated with RNA unfolding as a function of time or the presence of
biochemical signals. We have been studying the mechanism of RNA remodeling by a class of enzymes that are involved in all
aspects of RNA metabolism and in viral replication: the DExH/D subgroup of helicase superfamily 2 (SF2). Although SF2
proteins were originally designated as "helicases" based on a phylogenetic analysis of conserved ATPase motifs, they display
a diversity of mechanical functions that contribute to cellular metabolism. Depending on the influence of auxiliary domains
and bound cofactors, the SF2 core can catalyze different types of conformational changes and nucleic acid rearrangements.
Many members of the DExH family often display processive single-strand translocation, which underlies their basic mechanism
for helicase activity. By contrast, the DEAD members are high-affinity ATP-dependent RNA-binding proteins that do not appear
to translocate along nucleic acids. DEAD proteins act as switches that can catalyze duplex annealing or displacement,
depending on the protein, the reaction conditions and the hydrolysis state of bound nucleotide. Many members of the SF2
family have evolved to function not as helicases, but as protein displacement enzymes that facilitate the remodeling of
large ribonucleoprotein (RNP) complexes. Others help catalyze the tertiary structural folding of large RNA molecules.
SF2 proteins therefore comprise a diverse group of adaptable motor enzymes that contribute to all aspects of cellular
function. We therefore refer to them as remodeling proteins rather than helicases (for a complete review of this topic,
see Pyle, A.M., Annu Rev Biophys, 2008).
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