Grip it and rip it: Structural mechanisms of DNA helicase substrate binding and unwinding

Bhattacharyya, Basudeb; Keck, James L.

doi:10.1002/pro.2533

Cited by 22 publications

(18 citation statements)

References 74 publications

(276 reference statements)

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“…This angle is larger than that in RecQ1, BLM, and other SF2 helicase/DNA complexes determined to date (20-60°) and instead is within the range observed in single-subunit SF1/DNA complexes (90-110°) (Fig. S8) (23). In the case of SF1 enzymes PcrA and UvrD, the angle at the ss/dsDNA bend has been proposed to help drive DNA unwinding by allowing the enzyme to peel ssDNA away from the duplex, although these enzymes also use wedge elements to assist in DNA unwinding (20,21).…”

Section: Discussioncontrasting

confidence: 41%

“…However, the equivalent β-hairpin in EcRecQ is much shorter and is dispensable for helicase activity (10,11), indicating that the bacterial and human RecQ proteins use different strand-separation mechanisms. This finding is even more surprising given that putative wedge elements have been identified in all other SF1 and SF2 DNA helicases of known structure (23). Understanding how bacterial RecQs function without a wedge element could offer new insights into the mechanisms by which helicases can unwind DNA.…”

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confidence: 99%

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Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Manthei

Hill

Burke

et al. 2015

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

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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...

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Section: Discussioncontrasting

confidence: 41%

mentioning

confidence: 99%

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Manthei

Hill

Burke

et al. 2015

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

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“…This general classification of DNA lesions can be useful for investigating the importance of helicase contacts with the DNA substrate during single-stranded DNA translocation or duplex DNA unwinding. As discussed recently in a review from the Keck laboratory [1], crystal structures of DNA helicases from the conserved Superfamily (SF)1 and SF2 along with mechanistic studies of helicase proteins have provide important insights to how they bind and unwind DNA. This has enabled researchers to conceptually visualize how structural elements of the helicase domain and other protein domains make dynamic contacts with the bases and sugar phosphate backbone to enact base-pair (bp) separation in a manner dependent on nucleoside triphosphate hydrolysis.…”

Section: Dna Lesions and Their Effects On Helicasesmentioning

confidence: 99%

Close encounters for the first time: Helicase interactions with DNA damage

2015

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DNA helicases are molecular motors that harness the energy of nucleoside triphosphate hydrolysis to unwinding structured DNA molecules that must be resolved during cellular replication, DNA repair, recombination, and transcription. In vivo, DNA helicases are expected to encounter a wide spectrum of covalent DNA modifications to the sugar phosphate backbone or the nitrogenous bases; these modifications can be induced by endogenous biochemical processes or exposure to environmental agents. The frequency of lesion abundance can vary depending on the lesion type. Certain adducts such as oxidative base modifications can be quite numerous, and their effects can be helix-distorting or subtle perturbations to DNA structure. Helicase encounters with specific DNA lesions and more novel forms of DNA damage will be discussed. We will also review the battery of assays that have been used to characterize helicase-catalyzed unwinding of damaged DNA substrates. Characterization of the effects of specific DNA adducts on unwinding by various DNA repair and replication helicases has proven to be insightful for understanding mechanistic and biological aspects of helicase function in cellular DNA metabolism.

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“…Translocases are molecular motors that couple the hydrolysis of nucleoside triphosphates, usually ATP, with movement along single-or double-stranded nucleic acid. Helicases are a type of nucleic acid translocase that couple this movement to unwinding of the strands within a nucleic acid duplex [14][15][16]. DNA unwinding at the replication fork is performed by hexameric helicases within the context of the replisome, with the hexameric rings encircling either the lagging or the leading strand template in bacteria and eukaryotes, respectively [17].…”

Section: The Problem With Nucleoprotein Complexesmentioning

confidence: 99%

“…All helicases demonstrated to accelerate fork movement along protein-bound DNA are members of helicase Superfamily 1, a class of helicases that translocate along ssDNA either with 3′-5′ or with 5′-3′ polarity [14][15][16]. These translocation properties imply that these helicases translocate along single-stranded template DNA at the fork to facilitate displacement of nucleoprotein barriers.…”

Section: Polaritymentioning

confidence: 99%

Accessory Replicative Helicases and the Replication of Protein-Bound DNA

Brüning

Howard

McGlynn

2014

Journal of Molecular Biology

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Complete, accurate duplication of the genetic material is a prerequisite for successful cell division. Achieving this accuracy is challenging since there are many barriers to replication forks that may cause failure to complete genome duplication or result in possibly catastrophic corruption of the genetic code. One of the most important types of replicative barriers are proteins bound to the template DNA, especially transcription complexes. Removal of these barriers demands energy input not only to separate the DNA strands but also to disrupt multiple bonds between the protein and DNA. Replicative helicases that unwind the template DNA for polymerases at the fork can displace proteins bound to the template. However, even occasional failures in protein displacement by the replicative helicase could spell disaster. In such circumstances, failure to restart replication could result in incomplete genome duplication. Avoiding incomplete genome duplication via the repair and restart of blocked replication forks also challenges viability since the involvement of recombination enzymes is associated with the risk of genome rearrangements. Organisms have therefore evolved accessory replicative helicases that aid replication fork movement along protein-bound DNA. These helicases reduce the dangers associated with replication blockage by protein-DNA complexes, aiding clearance of blocks and resumption of replication by the same replisome thus circumventing the need for replication repair and restart. This review summarises recent work in bacteria and eukaryotes that has begun to delineate features of accessory replicative helicases and their importance in genome stability.

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Grip it and rip it: Structural mechanisms of DNA helicase substrate binding and unwinding

Cited by 22 publications

References 74 publications

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Close encounters for the first time: Helicase interactions with DNA damage

Accessory Replicative Helicases and the Replication of Protein-Bound DNA

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