Dda Helicase Tightly Couples Translocation on Single-Stranded DNA to Unwinding of Duplex DNA: Dda Is an Optimally Active Helicase (original) (raw)
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Mechanisms of Helicase-Catalyzed DNA Unwinding
Annual Review of Biochemistry, 1996
DNA helicases are essential motor proteins that function to unwind duplex DNA to yield the transient single-stranded DNA intermediates required for replication, recombination, and repair. These enzymes unwind duplex DNA and translocate along DNA in reactions that are coupled to the binding and hydrolysis of 5′-nucleoside triphosphates (NTP). Although these enzymes are essential for DNA metabolism, the molecular details of their mechanisms are only beginning to emerge. This review discusses mechanistic aspects of helicasecatalyzed DNA unwinding and translocation with a focus on energetic (thermodynamic), kinetic, and structural studies of the few DNA helicases for which such information is available. Recent studies of DNA and NTP binding and DNA unwinding by the Escherichia coli (E. coli) Rep helicase suggest that the Rep helicase dimer unwinds DNA by an active, rolling mechanism. In fact, DNA helicases appear to be generally oligomeric (usually dimers or hexamers), which provides th...
Helicase-catalyzed DNA unwinding: energy coupling by DNA motor proteins
Biophysical Journal, 1995
DNA helicases catalyze the unwinding of double-stranded (ds) DNA to yield the single-stranded (ss) DNA intermediates required in DNA replication, recombination, and repair. DNA helicases couple the free energy of nucleoside triphosphate (NTP) binding and hydrolysis to separate the two complementary DNA strands while also translocating vectorially along the DNA substrate. As such, helicases are functionally DNA motor proteins. The functional form of helicases generally appears to be oligomeric (usually dimers or hexamers), which provides the helicase with multiple DNA binding sites that are required for translocation and DNA unwinding. The affinity of ss-versus dsDNA for these multiple DNA binding sites is modulated allosterically by NTP binding, hydrolysis, and product release, which is central to helicase-catalyzed DNA unwinding. The mechanistic details of the DNA unwinding, translocation, and NTPase reactions are only starting to emerge. We discuss energy coupling by DNA helicases in general, and by the dimeric E. coli Rep helicase in particular, focusing on the similarities of these enzymes to classical motor proteins.
Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase
UvrD, a model for non-hexameric Superfamily 1 helicases, utilizes ATP hydrolysis to translocate stepwise along single-stranded DNA and unwind the duplex. To dissect the mechanism underlying DNA unwinding, we use optical tweezers to measure directly the stepping behavior of UvrD as it processes a DNA hairpin and show that UvrD exhibits a variable step size averaging ~3 base pairs. Analyzing stepping kinetics across ATP reveals the type and number of catalytic events that occur with different step sizes. These single-molecule data reveal a mechanism in which UvrD moves one base pair at a time but sequesters the nascent single strands, releasing them non-uniformly after a variable number of catalytic cycles. Molecular dynamics simulations point to a structural basis for this behavior, identifying the protein-DNA interactions responsible for strand sequestration. Based on structural and sequence alignment data, we propose that this stepping mechanism may be conserved among other non-hex...
Journal of Molecular Biology, 2002
DNA helicases are molecular motors that use the energy from NTP hydrolysis to drive the process of duplex DNA strand separation. Here, we measure the translocation and energy coupling efficiency of a replicative DNA helicase from bacteriophage T7 that is a member of a class of helicases that assembles into ring-shaped hexamers. Presteady state kinetics of DNA-stimulated dTTP hydrolysis activity of T7 helicase were measured using a real time assay as a function of ssDNA length, which provided evidence for unidirectional translocation of T7 helicase along ssDNA. Global fitting of the kinetic data provided an average translocation rate of 132 bases per second per hexamer at 18 8C. While translocating along ssDNA, T7 helicase hydrolyzes dTTP at a rate of 49 dTTP per second per hexamer, which indicates that the energy from hydrolysis of one dTTP drives unidirectional movement of T7 helicase along two to three bases of ssDNA. One of the features that distinguishes this ring helicase is its processivity, which was determined to be 0.99996, which indicated that T7 helicase travels on an average about 75 kb of ssDNA before dissociating. We propose that the ability of T7 helicase to translocate unidirectionally along ssDNA in an efficient manner plays a crucial role in DNA unwinding.
Helicase-catalyzed DNA unwinding
The Journal of biological chemistry, 1993
DNA helicases are ubiquitous and multiple helicases have been identified in a number of prokaryotes and eukaryotes. Although it is clear that not all helicases function identically, many of these enzymes possess similar properties that appear to be of general importance for their mechanism of action. For example, the assembly states of most (possibly all) helicases are oligomeric. The prime consequence of an oligomeric helicase is that it possesses multiple DNA binding sites, a feature that is required for any "active" mechanism of DNA unwinding, since it enables a helicase to bind both ss- and duplex DNA or two strands of ss-DNA simultaneously at an unwinding fork. Modulation of the relative affinities of ss- versus duplex DNA for these multiple binding sites through ATP binding and hydrolysis, as has been observed for the E. coli Rep dimer, can provide a mechanism for translocation and processive unwinding of DNA. Along with studies of DNA unwinding, further understandin...
Helicase on DNA: a phase coexistence based mechanism
We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch ensemble that entails a coexistence of domains of zipped and unzipped phases of DNA, separated by a domain wall. The motor action of the helicase leads to a change in the position of the fixed constraint thereby shifting the domain wall on dsDNA. We associate this off-equilibrium domain wall motion with the unzipping activity of helicase. We show that this proposal gives a clear and consistent explanation of the main observed features of helicases.
DNA synthesis provides the driving force to accelerate DNA unwinding by a helicase
Nature, 2005
Helicases are molecular motors that use the energy of nucleoside 5 0 -triphosphate (NTP) hydrolysis to translocate along a nucleic acid strand and catalyse reactions such as DNA unwinding. The ring-shaped helicase 1 of bacteriophage T7 translocates along single-stranded (ss)DNA at a speed of 130 bases per second 2 ; however, T7 helicase slows down nearly tenfold when unwinding the strands of duplex DNA 3 . Here, we report that T7 DNA polymerase, which is unable to catalyse strand displacement DNA synthesis by itself, can increase the unwinding rate to 114 base pairs per second, bringing the helicase up to similar speeds compared to its translocation along ssDNA. The helicase rate of stimulation depends upon the DNA synthesis rate and does not rely on specific interactions between T7 DNA polymerase and the carboxy-terminal residues of T7 helicase. Efficient duplex DNA synthesis is achieved only by the combined action of the helicase and polymerase. The strand displacement DNA synthesis by the DNA polymerase depends on the unwinding activity of the helicase, which provides ssDNA template. The rapid trapping of the ssDNA bases by the DNA synthesis activity of the polymerase in turn drives the helicase to move forward through duplex DNA at speeds similar to those observed along ssDNA.
SURVEY AND SUMMARY DNA mechanics as a tool to probe helicase and translocase activity
2006
Helicases and translocases are proteins that use the energy derived from ATP hydrolysis to move along or pump nucleic acid substrates. Single molecule manipulation has proved to be a powerful tool to investigate the mechanochemistry of these motors. Here we first describe the basic mechanical properties of DNA unraveled by single molecule manipulation techniques. Then we demonstrate how the knowledge of these properties has been used to design single molecule assays to address the enzymatic mechanisms of different translocases. We report on four single molecule manipulation systems addressing the mechanism of different helicases using specifically designed DNA substrates: UvrD enzyme activity detection on a stretched nicked DNA molecule, HCV NS3 helicase unwinding of a RNA hairpin under tension, the observation of RecBCD helicase/nuclease forward and backward motion, and T7 gp4 helicase mediated opening of a synthetic DNA replication fork. We then discuss experiments on two dsDNA translocases: the RuvAB motor studied on its natural substrate, the Holliday junction, and the chromosome-segregation motor FtsK, showing its unusual coupling to DNA supercoiling.
DNA Mechanics As a Tool to Probe Helicase and Translocase Activity
Nucleic acids …, 2006
Helicases and translocases are proteins that use the energy derived from ATP hydrolysis to move along or pump nucleic acid substrates. Single molecule manipulation has proved to be a powerful tool to investigate the mechanochemistry of these motors. Here we first describe the basic mechanical properties of DNA unraveled by single molecule manipulation techniques. Then we demonstrate how the knowledge of these properties has been used to design single molecule assays to address the enzymatic mechanisms of different translocases. We report on four single molecule manipulation systems addressing the mechanism of different helicases using specifically designed DNA substrates: UvrD enzyme activity detection on a stretched nicked DNA molecule, HCV NS3 helicase unwinding of a RNA hairpin under tension, the observation of RecBCD helicase/nuclease forward and backward motion, and T7 gp4 helicase mediated opening of a synthetic DNA replication fork. We then discuss experiments on two dsDNA translocases: the RuvAB motor studied on its natural substrate, the Holliday junction, and the chromosome-segregation motor FtsK, showing its unusual coupling to DNA supercoiling.
F1000 - Post-publication peer review of the biomedical literature, 2007
Helicases use the energy derived from nucleoside triphosphate hydrolysis to unwind double helices in essentially every metabolic pathway involving nucleic acids. Earlier crystal structures have suggested that DNA helicases translocate along a single-stranded DNA in an inchworm fashion. We report here a series of crystal structures of the UvrD helicase complexed with DNA and ATP hydrolysis intermediates. These structures reveal that ATP binding alone leads to unwinding of 1 base pair by directional rotation and translation of the DNA duplex and ADP and Pi release leads to translocation of the developing single strand. Thus DNA unwinding is achieved by a two-part power stroke in a combined wrench-and-inchworm mechanism. The rotational angle and translational distance of DNA define the unwinding step to be 1 base pair per ATP hydrolyzed. Finally, a gateway for ssDNA translocation and an alternative strand displacement mode may explain the varying step sizes previously reported.