Escherichia coli helicase II (UvrD) protein initiates DNA unwinding at nicks and blunt ends.

Runyon, Gregory T.; Bear, David G.; Lohman, Timothy M.

doi:10.1073/pnas.87.16.6383

Cited by 101 publications

(87 citation statements)

References 39 publications

(36 reference statements)

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“…1). Note that our observation of preferential translocation of UvrD along the continuous DNA strand at a nick contrasts with the bidirectional movement of UvrD from such a structure reported previously (66). This discrepancy might reflect the use of a large excess of UvrD in relation to DNA substrate used in the previous report.…”

Section: Discussioncontrasting

confidence: 56%

Stimulation of UvrD Helicase by UvrAB

Atkinson

Guy

Cadman

et al. 2009

Journal of Biological Chemistry

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Helicases play critical roles in all aspects of nucleic acid metabolism by catalyzing the remodeling of DNA and RNA structures. UvrD is an abundant helicase in Escherichia coli with well characterized functions in mismatch and nucleotide excision repair and a possible role in displacement of proteins such as RecA from single-stranded DNA. Helicases and translocases use the energy derived from NTP hydrolysis to translocate along single-stranded or doublestranded nucleic acids to remodel nucleic acid structures. Many of these enzymes have RecA-like motor domains, reflecting close similarities in translocation mechanisms (1-3). Specificity is often, therefore, conferred by additional domains within these motor enzymes (4). It is also becoming apparent that helicases and translocases often function as part of larger multisubunit complexes rather than in isolation and that such interactions impact on motor function and specificity. The complex interactions between replicative helicases and other proteins acting at the replication fork have long been known to be critical for replisome function (5-7). Many helicases also interact with, and their activities modulated by, ssDNA 2 -binding proteins (8 -13), while helicase/translocase interactions with RNA polymerases are emerging (14, 15).The Escherichia coli 3Ј-5Ј helicase UvrD (16) has roles in mismatch (17) and nucleotide excision repair (18) and may also act to displace proteins such as RecA at replication forks or ssDNA gaps in duplex DNA (19 -21). UvrD is likely the most abundant helicase in E. coli (22). There is also a second helicase in E. coli, Rep, that shares 40% identity with UvrD but has no known role in mismatch or nucleotide excision repair or in protein displacement in vivo. Employment of UvrD, but not Rep, in a diversity of roles in vivo might, therefore, demand specific physical or functional interactions between UvrD and other proteins in each system. However, specific interaction of UvrD has only been documented with a component of the mismatch repair system, MutL (23). This interaction appears to be essential in allowing a motor with limited dsDNA processivity to unwind the large tracts of DNA necessary during mismatch repair (23)(24)(25)(26).Little is known concerning the protein displacement function of UvrD in vivo. Lack of UvrD leads to a hyperrecombination phenotype (27), whereas UvrD can both promote (20,21) and inhibit (20) RecA-catalyzed strand exchange in vitro, depending on reaction conditions. UvrD might, therefore, promote turnover of RecA-ssDNA complexes at blocked forks and gaps in duplex DNA. Inhibition of RecA function at blocked forks might facilitate other pathways of fork repair that do not rely on strand exchange, possibly minimizing the risks to genome stability that blocked forks present (28). However, whether abortion of strand exchange by UvrD in vivo requires other proteins is unknown. In contrast, the role of UvrD in nucleotide excision repair is well characterized. Nucleotide excision repair is needed to remove and replace ...

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Section: Discussioncontrasting

confidence: 56%

Stimulation of UvrD Helicase by UvrAB

Atkinson

Guy

Cadman

et al. 2009

Journal of Biological Chemistry

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“…3A). This result was, perhaps, unexpected because UvrD has been shown to be capable of initiating an unwinding reaction at a blunt end (28,38). If UvrD were initiating the unwinding of the HJ substrate at one of the blunt ends then we would have expected to observe significant accumulation of a three-stranded product (Fig.…”

Section: Resultsmentioning

confidence: 78%

Resolving Holliday Junctions with Escherichia coli UvrD Helicase

Tahmaseb

Compton

et al. 2012

Journal of Biological Chemistry

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“…Its ATPdependent activities include translocation along single-stranded (ss) DNA (12)(13)(14)(15)(16), duplex DNA unwinding (17)(18)(19)(20)(21)(22), displacement of RecA filaments from ssDNA (10,11), and pushing of proteins along ssDNA (23).…”

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confidence: 99%

Large Domain Movements Upon UvrD Dimerization and Helicase Activation

Nguyen

Ordabayev

Sokoloski

et al. 2018

Biophysical Journal

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Escherichia coli UvrD DNA helicase functions in several DNA repair processes. As a monomer, UvrD can translocate rapidly and processively along ssDNA; however, the monomer is a poor helicase. To unwind duplex DNA in vitro, UvrD needs to be activated either by self-assembly to form a dimer or by interaction with an accessory protein. However, the mechanism of activation is not understood. UvrD can exist in multiple conformations associated with the rotational conformational state of its 2B subdomain, and its helicase activity has been correlated with a closed 2B conformation. Using single-molecule total internal reflection fluorescence microscopy, we examined the rotational conformational states of the 2B subdomain of fluorescently labeled UvrD and their rates of interconversion. We find that the 2B subdomain of the UvrD monomer can rotate between an open and closed conformation as well as two highly populated intermediate states. The binding of a DNA substrate shifts the 2B conformation of a labeled UvrD monomer to a more open state that shows no helicase activity. The binding of a second unlabeled UvrD shifts the 2B conformation of the labeled UvrD to a more closed state resulting in activation of helicase activity. Binding of a monomer of the structurally similar Escherichia coli Rep helicase does not elicit this effect. This indicates that the helicase activity of a UvrD dimer is promoted via direct interactions between UvrD subunits that affect the rotational conformational state of its 2B subdomain.single molecule | conformational heterogeneity | DNA motors | DNA repair U vrD from Escherichia coli is a nonhexameric SF1A DNA helicase/translocase, structurally similar to E. coli Rep and Bacillus stearothermophilus PcrA, which is involved in many aspects of genome maintenance (1, 2), including DNA repair (3, 4), replication (5-8), and recombination (7, 9-11). Its ATPdependent activities include translocation along single-stranded (ss) DNA (12-16), duplex DNA unwinding (17-22), displacement of RecA filaments from ssDNA (10, 11), and pushing of proteins along ssDNA (23).The activities of UvrD can be modulated in vitro by its assembly state and/or by binding partners (1). UvrD monomers can translocate directionally (3′ to 5′) along ssDNA [∼190 nucleotides (nts) s −1 ] (12, 13, 15, 16), in a reaction that is tightly coupled to ATP hydrolysis (14). However, UvrD monomers show little helicase activity (12,16,21,24,25). In the absence of accessory proteins, helicase activity in vitro requires formation of a UvrD dimer (16,21,(25)(26)(27). The dimer unwinds dsDNA with rates of ∼70 base pair (bp) s −1 (20,21,24,27). Rep and PcrA monomers also show no helicase activity and require oligomerization or an accessory protein for helicase activity in vitro (28-31).UvrD, Rep, and PcrA all contain four subdomains (1A, 2A, 1B, and 2B) (2,(32)(33)(34)(35), and the 2B subdomain can undergo a substantial rotation about a hinge region connecting it to the 2A subdomain (2,22,(32)(33)(34)(35)(36)(37). A structure of an apo UvrD monome...

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Escherichia coli helicase II (UvrD) protein initiates DNA unwinding at nicks and blunt ends.

Cited by 101 publications

References 39 publications

Stimulation of UvrD Helicase by UvrAB

Stimulation of UvrD Helicase by UvrAB

Resolving Holliday Junctions with Escherichia coli UvrD Helicase

Large Domain Movements Upon UvrD Dimerization and Helicase Activation

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