DNA binding to RecD: role of the 1B domain in SF1B helicase activity

Saikrishnan, K.; Griffiths, Stuart P; Cook, Nicola; Court, Robert; Wigley, Dale B.

doi:10.1038/emboj.2008.144

Cited by 89 publications

(133 citation statements)

References 43 publications

Supporting

Mentioning

124

Contrasting

Order By: Relevance

“…Cycling between these states with alternating ssDNA binding at each site is thought to drive helicase translocation via an inchworm mechanism. Similar mechanisms have been proposed for SF1 helicases (20,21,43). In EcRecQ and CsRecQ, Thr293 provides one of the equivalent Thr residues, whereas Arg125 replaces the second Thr.…”

Section: Discussionmentioning

confidence: 84%

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Manthei

Hill

Burke

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. Here, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3′ single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ∼90°to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATP hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. This bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.helicase | RecQ | mechanism | aromatic-rich loop | DNA bending H elicases are motor proteins that convert the chemical energy of nucleoside triphosphate (NTP) hydrolysis into the mechanical energy needed to separate nucleic acid strands (1). The largest and most diverse helicase superfamilies, SF1 and SF2, use conserved sequence motifs (I, Ia, II-VI) within their helicase domains to couple NTP hydrolysis to conformational changes that mediate DNA translocation and unwinding (1, 2). Although the DNA-unwinding mechanisms of SF1 helicases have been examined extensively, far less is known about SF2 enzymes, in part because of the smaller number of available helicase/substrate complex structures.RecQ DNA helicases are SF2 enzymes with broad roles in promoting genomic stability in eubacterial and eukaryotic species (3). Their importance is underscored by the multiple genomic instability diseases caused by mutations in human recQ genes (4-8). At a structural level, most RecQ helicases share a similar domain architecture that includes a helicase domain, a RecQ C-terminal (RQC) element comprised of Zn 2+ -binding and winged-helix (WH) domains, and a helicase and RNaseD C-terminal (HDRC) domain (Fig. 1A) (9, 10). The helicase and RQC domains combine to form a catalytic core that is sufficient for DNA-unwinding activity in many RecQ proteins. Crystal structures of several RecQ catalytic cores have been determined, including Escherichia coli RecQ (EcRecQ), human RecQ1, and human Bloom syndrome protein (BLM) [refs. 10-12 and unpublished structures (4CDG, 2WWY, and 4CGZ) available through the Protein Data Bank (PDB)]. A comparison of these structures reveals strong similarities among domains within the catalytic core but also differences in the relative positioning of these domains among RecQ proteins. The EcRecQ and antibody-bound BLM structures form an open arrangement in which the WH domain is centered relative to the helicase and Zn 2+ -binding domains, but in RecQ1 and DNA-bound BLM a closed arrangement is observed with the WH domain positioned laterally to the helicase domain (Fig. 1B and Fig. S1) (10-12). The functional relevance of...

show abstract

Section: Discussionmentioning

confidence: 84%

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Manthei

Hill

Burke

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…1 B, i, compare lanes 10 and 11 with lanes 3 and 2, and 1 B, ii). However, a mutant RecD2 protein, pinless RecD2, that retains DNA binding but not helicase activity (23) failed to inhibit resumption of replication (Fig. 1C).…”

Section: Recd2 Inhibits Resumption Of Replication By Paused Replisomesmentioning

confidence: 99%

Protein–DNA complexes are the primary sources of replication fork pausing in Escherichia coli

Gupta

Guy

Yeeles

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

105

View full text Add to dashboard Cite

Replication fork pausing drives genome instability, because any loss of paused replisome activity creates a requirement for reloading of the replication machinery, a potentially mutagenic process. Despite this importance, the relative contributions to fork pausing of different replicative barriers remain unknown. We show here that Deinococcus radiodurans RecD2 helicase inactivates Escherichia coli replisomes that are paused but still functional in vitro, preventing continued fork movement upon barrier removal or bypass, but does not inactivate elongating forks. Using RecD2 to probe replisome pausing in vivo, we demonstrate that most pausing events do not lead to replisome inactivation, that transcription complexes are the primary sources of this pausing, and that an accessory replicative helicase is critical for minimizing the frequency and/or duration of replisome pauses. These findings reveal the hidden potential for replisome inactivation, and hence genome instability, inside cells. They also demonstrate that efficient chromosome duplication requires mechanisms that aid resumption of replication by paused replisomes, especially those halted by protein-DNA barriers such as transcription complexes.DNA repair | genome stability | Rep | RNA polymerase | recombination

show abstract

“…Some of the well-characterized SF1A helicases are PcrA, Rep, and UvrD T [87][88][89][90][91][92]. Well-characterized members of SF1B include RecD and Dda [93,94] (He et al, in press). The biological functions, polarity, and active forms of some of the SF1 helicases are listed (Table 2.2).…”

Section: Superfamily 1 Helicasesmentioning

confidence: 99%

“…Domains 1A and 2A have the RecA-like fold seen in all SF1 and SF2 helicases [48]. Domain 1B forms a rigid -hairpin that protrudes from the surface of domain 1A, and the 2B domain has an SH3 fold [93]. The ssDNA-binding site runs in a 5 -3 direction along a channel across the top of domains 2A and 1A.…”

Section: Structure Of Sf1b Helicases (Recd2 and Dda)mentioning

confidence: 99%

“…For the SF1B helicase Dda, mutation of a single F residue in the pin which stacks with the ssDNA completely eliminates strand separation although translocation on ssDNA is unaffected. In the case of RecD2 [93], the pin is short and it appears to function only in splitting the incoming duplex. Dda contains a long -hairpin which is anchored at its tip by electrostatic interactions to domain 2B, allowing it to function not only directly in splitting the dsDNA but also in coupling ATP hydrolysis to unwinding (He et al, in press).…”

Section: Duplex Dna Is Split By the Pin Regionmentioning

confidence: 99%

See 1 more Smart Citation

Erratum to: Structure and Mechanisms of SF1 DNA Helicases

Raney

Byrd

Aarattuthodiyil

2012

Advances in Experimental Medicine and Biology

View full text Add to dashboard Cite

Superfamily I is a large and diverse group of monomeric and dimeric helicases defined by a set of conserved sequence motifs. Members of this class are involved in essential processes in both DNA and RNA metabolism in all organisms. In addition to conserved amino acid sequences, they also share a common structure containing two RecA-like motifs involved in ATP binding and hydrolysis and nucleic acid binding and unwinding. Unwinding is facilitated by a "pin" structure which serves to split the incoming duplex. This activity has been measured using both ensemble and single-molecule conditions. SF1 helicase activity is modulated through interactions with other proteins.

show abstract

DNA binding to RecD: role of the 1B domain in SF1B helicase activity

Cited by 89 publications

References 43 publications

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Protein–DNA complexes are the primary sources of replication fork pausing in Escherichia coli

Erratum to: Structure and Mechanisms of SF1 DNA Helicases

Contact Info

Product

Resources

About