Structural Basis for DNA Strand Separation by the Unconventional Winged-Helix Domain of RecQ Helicase WRN

Kitano, Katsuhisa; Kim, Sunyong; Hakoshima, Toshio

doi:10.1016/j.str.2009.12.011

Cited by 109 publications

(171 citation statements)

References 37 publications

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“…The helicase domain also contacted the duplex, with interactions formed between residues 220-225 and the phosphodiester backbone. As was anticipated from biochemical experiments (11), the β-hairpin wedge found in human RecQ proteins (11,12,22,26) was shorter in CsRecQ and made only limited contacts with the DNA, and no other wedge element was observed (Fig. 2B).…”

Section: Significancesupporting

confidence: 79%

“…Structural and mutagenesis data have revealed differences between eukaryotic and bacterial RecQ unwinding in their reliance on a β-hairpin wedge within the WH domain. The β-hairpin in RecQ1, BLM, and WRN projects away from the WH to split DNA at the ss/dsDNA junction, and mutations in DNA-binding residues within the hairpin essentially eliminate DNA unwinding (11,12,22). In contrast, the β-hairpin in the bacterial RecQ WH domain is much shorter, and, although the CsRecQ/DNA structure shows that it also associates with the DNA backbone (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, the β-hairpin in the bacterial RecQ WH domain is much shorter, and, although the CsRecQ/DNA structure shows that it also associates with the DNA backbone (Fig. 2), mutations that substitute or delete the β-hairpin residue that binds DNA (His489) have negligible effects on DNA unwinding (11,22). How bacterial RecQs unwind DNA in the absence of an apparent wedge element therefore was unknown.…”

Section: Discussionmentioning

confidence: 99%

“…2B) (11,12,22). Loops from the WH domain (residues 432-434 and 441-446) and His489 from the WH β-hairpin contacted the phosphodiester backbone on either side of the DNA major groove ( Fig.…”

Section: Significancementioning

confidence: 99%

“…A third puzzling feature of RecQs is their varied use of a WH domain β-hairpin in DNA unwinding. In eukaryotic RecQ helicases, this β-hairpin projects away from the WH domain, forming a wedge that appears to separate DNA strands (11,12,22). 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.…”

mentioning

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: Significancesupporting

confidence: 79%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Significancementioning

confidence: 99%

mentioning

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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Can Designer Indels Be Tailored by Gene Editing?

et al. 2019

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Genome editing with engineered nucleases (GEENs) introduce site-specific DNA double-strand breaks (DSBs) and repairs DSBs via nonhomologous end-joining (NHEJ) pathways that eventually create indels (insertions/ deletions) in a genome. Whether the features of indels resulting from gene editing could be customized is asked. A review of the literature reveals how gene editing technologies via NHEJ pathways impact gene editing. The survey consolidates a body of literature that suggests that the type (insertion, deletion, and complex) and the approximate length of indel edits can be somewhat customized with different GEENs and by manipulating the expression of key NHEJ genes. Structural data suggest that binding of GEENsto DNA may interfere with binding of key components of DNA repair complexes, favoring either classical-or alternative-NHEJ. The hypotheses have some limitations, but if validated, will enable scientists to better control indel makeup, holding promise for basic science and clinical applications of gene editing. Also see the video abstract here https://youtu.be/vTkJtUsLi3w

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Backbone Dynamics and Model‐Free Analysis of the RecQ C‐Terminal Domain of Bloom Syndrome Protein

Yoo

Lee

Park

2018

Bulletin Korean Chem Soc

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Bloom syndrome protein (BLM) is one of RecQ helicases, which are conserved DNA unwinding enzymes in DNA metabolisms. The RecQ C-terminal domain (RQC) of BLM is a winged-helix motif, which recognizes various DNA structures. BLM RQC mediates electrostatic interactions with duplex DNA by using polar residues in the β-wing and α2-α3 loop. In order to understand the dynamic properties of RQC for recognizing its substrate DNA, we measured 15 N spin relaxation parameters of the protein and performed model-free analysis. Our results showed that the β-wing region, which is used for the strand separation, has flexible backbone structure. The α2-α3 loop, the binding surface of the DNA major groove, was found to be relatively rigid. Our results contribute to a better understanding of molecular basis of BLM RQC-DNA interaction.

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Structural Basis for DNA Strand Separation by the Unconventional Winged-Helix Domain of RecQ Helicase WRN

Cited by 109 publications

References 37 publications

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Can Designer Indels Be Tailored by Gene Editing?

Backbone Dynamics and Model‐Free Analysis of the RecQ C‐Terminal Domain of Bloom Syndrome Protein

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