The ATPase Cycle of PcrA Helicase and Its Coupling to Translocation on DNA

Toseland, Christopher P.; Martinez-Senac, Maria M.; Slatter, Andrew F.; Webb, Martin R.

doi:10.1016/j.jmb.2009.07.071

Cited by 37 publications

(54 citation statements)

References 42 publications

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“…Furthermore, it is tempting to conclude that the resolution of small ssDNA loops formed by PcrA is the rate-limiting process associated with the ∼4 nucleotide kinetic step-size. An inchworm model for ssDNA translocation by PcrA is also consistent with the observation that the products of ATP hydrolysis associated with PcrA translocation along ssDNA are released in two steps, with P i released before ADP (54). Based on this result it has been suggested that the major transition in the structure of the PcrA:DNA complex, possibly associated with the powerstroke of the translocation mechanism (Figure 2), is associated with ADP release.…”

Section: Sf1 Family Helicasessupporting

confidence: 81%

All motors have to decide is what to do with the DNA that is given them

Briggs

Fischer

2014

Biomolecular Concepts

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DNA translocases are a diverse group of molecular motors responsible for a wide variety of cellular functions. The goal of this review is to identify common aspects in the mechanisms for how these enzymes couple the binding and hydrolysis of ATP to their movement along DNA. Not surprisingly, the shared structural components contained within the catalytic domains of several of these motors appear to give rise to common aspects of DNA translocation. Perhaps more interesting, however, are the differences between the families of translocases and the potential associated implications both for the functions of the members of these families and for the evolution of these families. However, as there are few translocases for which complete characterizations of the mechanisms of DNA binding, DNA translocation, and DNA-stimulated ATPase have been completed, it is difficult to form many inferences. We therefore hope that this review motivates the necessary further experimentation required for broader comparisons and conclusions.

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Section: Sf1 Family Helicasessupporting

confidence: 81%

All motors have to decide is what to do with the DNA that is given them

Briggs

Fischer

2014

Biomolecular Concepts

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“…Utp14 also increases the coupling between ATP hydrolysis and productive unwinding by Dhr1, because the presence of Utp14 stimulates unwinding activity by Dhr1 without affecting rates of ATPase hydrolysis. A possible molecular basis of such stimulation is provided by the DNA helicase PcrA, whose activator, RepD, stimulates the unwinding of PcrA without affecting ATPase activity (38,39). RepD exploits a common feature of the reaction cycle of helicases with tandem RecA-like domains-these domains cycle between an open, inactive conformation and a closed, active conformation (40).…”

Section: Discussionmentioning

confidence: 99%

“…In the active form, the two RecA-like domains come together to form the NTP and RNA duplex binding cleft. Cross-linking and fluorescence resonance energy transfer (FRET) studies suggest that RepD stimulates the helicase activity of PcrA by locking the tandem RecA-like domains in an active, closed conformation (39), and this is accomplished without stimulated ATPase activity (38). Perhaps the Utp14 contact to Dhr1 similarly stabilizes a closed conformation of the RecA-like domains of Dhr1 to couple unwinding to ATPase activity.…”

Section: Discussionmentioning

confidence: 99%

Utp14 Recruits and Activates the RNA Helicase Dhr1 To Undock U3 snoRNA from the Preribosome

Zhu

Liu

Anjos

et al. 2016

Molecular and Cellular Biology

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bIn eukaryotic ribosome biogenesis, U3 snoRNA base pairs with the pre-rRNA to promote its processing. However, U3 must be removed to allow folding of the central pseudoknot, a key feature of the small subunit. Previously, we showed that the DEAH/ RHA RNA helicase Dhr1 dislodges U3 from the pre-rRNA. DHR1 can be linked to UTP14, encoding an essential protein of the preribosome, through genetic interactions with the rRNA methyltransferase Bud23. Here, we report that Utp14 regulates Dhr1. Mutations within a discrete region of Utp14 reduced interaction with Dhr1 that correlated with reduced function of Utp14. These mutants accumulated Dhr1 and U3 in a pre-40S particle, mimicking a helicase-inactive Dhr1 mutant. This similarity in the phenotypes led us to propose that Utp14 activates Dhr1. Indeed, Utp14 formed a complex with Dhr1 and stimulated its unwinding activity in vitro. Moreover, the utp14 mutants that mimicked a catalytically inactive dhr1 mutant in vivo showed reduced stimulation of unwinding activity in vitro. Dhr1 binding to the preribosome was substantially reduced only when both Utp14 and Bud23 were depleted. Thus, Utp14 is bifunctional; together with Bud23, it is needed for stable interaction of Dhr1 with the preribosome, and Utp14 activates Dhr1 to dislodge U3. Ribosomes are complex ribonucleoprotein (RNP) particles composed of an intricate assembly of folded rRNA interdigitated with ribosomal proteins (r-proteins). Faithful assembly of this RNP is critical for efficient and accurate cellular translation. Eukaryotic cells devote more than 200 trans-acting factors (1-3) to the assembly of ribosomes. This highly dynamic process (4) involves extensive structural rearrangements of RNA-RNA, RNA-protein, and protein-protein interactions (5, 6). To investigate how structural rearrangements are regulated to occur at the proper stage of assembly, our studies centered on the RNA helicase Dhr1, which dissociates a key RNA-RNA interaction, dislodging U3 snoRNA from the pre-rRNA of the preribosome (1, 3, 7).U3 is instrumental in orchestrating early pre-rRNA processing. Ribosome assembly in Saccharomyces cerevisiae begins with the cotranscriptional assembly of the 90S preribosome, a large complex of r-proteins and trans-acting factors, including proteins and snoRNAs, on the growing 5= end of the nascent 35S transcript (8-10). The pre-rRNA undergoes extensive modification and processing (11) to liberate the mature 18S, 5.8S, and 25S rRNAs that are embedded between transcribed spacer elements. U3 snoRNA is required for the early cleavages at sites A0 and A1 to generate the mature 5= end of 18S and cleavage at A2 to separate the pre-40S (containing 20S pre-rRNA) from the pre-60S subunits (12, 13). Under conditions in which cleavage at A2 is blocked or reduced, cleavage at A3 can generate the pre-60S precursor. Thus, U3 is required for biogenesis of the small but not the large subunit.U3 is also expected to promote proper rRNA folding. U3 hybridizes with the pre-rRNA at multiple sites within the 35S precursor: at sites ...

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“…The mechanism for duplex unwinding exhibited by many helicases, including Pif1, is a stepwise, 1 base pair per step movement coupled to the hydrolysis of one molecule of ATP (44,59). The mechanism for other helicases has been suggested to involve buildup of strain so that multiple ATP hydrolysis events can occur followed by unzipping of 2 or more base pairs per step (60).…”

Section: Discussionmentioning

confidence: 99%

A Parallel Quadruplex DNA Is Bound Tightly but Unfolded Slowly by Pif1 Helicase

Byrd

Raney

2015

Journal of Biological Chemistry

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Background: Some G-rich sequences fold into intramolecular quadruplex structures. Pif1 helicase reduces genomic instability by unfolding quadruplex DNA. Results: Pif1 unfolds a parallel quadruplex structure slowly relative to unwinding of duplex DNA. Conclusion:Comparison of duplex unwinding to quadruplex unfolding is complicated by distinct kinetic mechanisms. Significance: A highly stable, intramolecular quadruplex is a formidable obstacle but can be overcome by Pif1 helicase.

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The ATPase Cycle of PcrA Helicase and Its Coupling to Translocation on DNA

Cited by 37 publications

References 42 publications

All motors have to decide is what to do with the DNA that is given them

All motors have to decide is what to do with the DNA that is given them

Utp14 Recruits and Activates the RNA Helicase Dhr1 To Undock U3 snoRNA from the Preribosome

A Parallel Quadruplex DNA Is Bound Tightly but Unfolded Slowly by Pif1 Helicase

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