Structure and Mechanism of Helicases and Nucleic Acid Translocases

Singleton, Martin R.; Dillingham, Mark S.; Wigley, Dale B.

doi:10.1146/annurev.biochem.76.052305.115300

Cited by 1,155 publications

(1,503 citation statements)

References 122 publications

Supporting

Mentioning

1,458

Contrasting

Unclassified

Order By: Relevance

“…This indicated a possible motor force for breaking histone-DNA contacts and moving DNA on the octamer surface. Notably, remodeler ATPases lack the 'pin' motif required for DNA strand separation and are therefore DNA translocases but not helicases 5,39 . One consistent feature of SF2 translocases is their tracking along the phosphate backbone of one of the two DNA strands, with limited interaction with the bases themselves 39,40 .…”

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

“…Notably, remodeler ATPases lack the 'pin' motif required for DNA strand separation and are therefore DNA translocases but not helicases 5,39 . One consistent feature of SF2 translocases is their tracking along the phosphate backbone of one of the two DNA strands, with limited interaction with the bases themselves 39,40 . Consistent with the notion of tracking, the results of triplex-displacement assays suggest that SWI/SNF, ISWI and Rad54 track in a 3′-to-5′ direction along one strand of the DNA duplex and are impeded if the tracking strand bears a gap in the phosphodiester backbone 4,36,38,41 .…”

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

“…Crystal structures, biochemical studies and single-molecule analyses of both SF1-and SF2-family translocases (PcrA, RecG, UvrD, NS3 and others) have provided many important insights into these issues 39,40,[57][58][59] . Currently, there is no crystal structure of the ATPase domain of a nucleosome-binding remodeler (SWI/SNF or ISWI), but recent structures of the SWI/SNF-family member Rad54 (with DNA) show remarkable structural homology to the SF2 family of RNA and DNA translocases (see Fig.…”

Section: Remodeler Atpases Resemble 'Dna Inchworms'mentioning

confidence: 99%

“…Although there is some diversity in their mechanisms, most monomeric SF1 and SF2 translocases conform to a 'DNA-inchworm' model of movement, which involves the coordinated movement of two domains: a DBD and a DNA-tracking domain 39,40 . The DNAtracking domain has two RecA-like motifs, and between them is a pocket for nucleotide binding as well as a platform for DNA interaction.…”

Section: Remodeler Atpases Resemble 'Dna Inchworms'mentioning

confidence: 99%

See 3 more Smart Citations

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

View full text Add to dashboard Cite

Chromatin remodelers are ATP-hydrolyzing machines specialized to restructure, mobilize or eject nucleosomes, allowing regulated exposure of DNA in chromatin. Recently, remodelers have been analyzed using single-molecule techniques in real time, revealing them to be complex DNA-pumping machines. The results both support and challenge aspects of current models of remodeling, supporting the idea that the remodeler translocates or pumps DNA loops into and around the nucleosome, while also challenging earlier concepts about loop formation, the character of the loop and how it propagates. Several complex behaviors were observed, such as reverse translocation and long translocation bursts of the remodeler, without appreciable DNA twist. This review presents and discusses revised models for nucleosome sliding and ejection that integrate this new information with the earlier biochemical studies.Many processes involving chromosomes are guided by DNA-binding proteins, and the access of these proteins to DNA is regulated by chromatin. Nucleosomes, the primary repeating unit of chromatin, package DNA by wrapping 147 base pairs (bp) around an octamer of histone proteins in ∼1.7 helical turns 1-3 . This packaging provides topological order but occludes one face of the DNA, which slows or prevents the recognition of DNA sequences by DNA-binding proteins. To maintain topological order, and also to allow rapid and regulated access to the DNA, cells have evolved a set of chromatin-remodeling machines that alter nucleosome position, presence and structure.Remodelers can be separated into several families on the basis of their composition and activities: SWI/SNF, ISWI, NURD/Mi-2/CHD and the 'split ATPases' INO80 and SWR1 (which bear an insertion within their ATPase domains). Rad54 may represent an additional family, as it perturbs chromatin in vitro, but it apparently lacks specific nucleosome-interacting domains 4,5 . The participation of remodelers in various chromosomal processes has been the subject of many reviews 6-9 . The present work focuses solely on remodeler mechanisms, and primarily on the function of their conserved catalytic subunit, a superfamily 2 (SF2) ATPdependent DNA translocase. Recently, single-molecule approaches have been used to examine several remodelers, providing many new insights into their behavior. Here I discuss these recent studies, compare them with previous biochemical studies and suggest refinements to existing models to account for some of the observations. Remodelers slide, eject and restructure nucleosomesRemodelers can affect nucleosomes in at least four ways ( Fig. 1): (i) sliding, or moving the histone octamer to a new position, which exposes DNA 10-12 ; (ii) ejection, or completely displacing the octamer to expose DNA [13][14][15][16] ; (iii) removal of H2A-H2B dimers, leaving only the central H3-H4 tetramer, which exposes DNA and destabilizes the nucleosome 17,18 ; and (iv) dimer replacement-for example, exchanging the resident H2A-H2B dimers for dimers NIH Public Access

show abstract

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

Section: Remodeler Atpases Resemble 'Dna Inchworms'mentioning

confidence: 99%

Section: Remodeler Atpases Resemble 'Dna Inchworms'mentioning

confidence: 99%

See 2 more Smart Citations

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

View full text Add to dashboard Cite

show abstract

“…RNA helicases are found in all three domains of life, and many viruses also encode one or more of these proteins 2,3 . Together with the structurally related DNA helicases that function in replication, recombination and repair, the RNA helicases are classified into superfamilies and families, based on sequence and structural features 3,4 . DEAD box proteins form the largest helicase family, with 37 members in humans and 26 in Saccharomyces cerevisiae 3 , and are characterized by the presence of an Asp-Glu-Ala-Asp (DEAD) motif.…”

mentioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

983

1,069

View full text Add to dashboard Cite

Nearly all aspects of RNA metabolism, from transcription and translation to mRNA decay, involve RNA helicases, which are enzymes that use ATP to bind or remodel RNA and RNA-protein complexes (ribonucleoprotein (RNP) complexes) 1 . RNA helicases are found in all three domains of life, and many viruses also encode one or more of these proteins 2,3 . Together with the structurally related DNA helicases that function in replication, recombination and repair, the RNA helicases are classified into superfamilies and families, based on sequence and structural features 3,4 . DEAD box proteins form the largest helicase family, with 37 members in humans and 26 in Saccharomyces cerevisiae 3 , and are characterized by the presence of an Asp-Glu-Ala-Asp (DEAD) motif.DEAD box helicases have central and, in many cases, essential physiological roles in cellular RNA metabolism 5 (FIG. 1). The proteins generally function as part of larger multicomponent assemblies, such as the spliceosom e or the eukaryotic translation initiation machinery 6 . Mutations and deregulation of several DEAD box proteins have been linked to disease states, including cancer 7 . Although all DEAD box proteins contain a structurally highly conserved core with conserved ATP-binding and RNA-binding sites, different proteins have been associated with diverse and seemingly unrelated functions, including the disassembly of RNPs, chaperoning during RNA folding and even stabil ization of protein complexes on RNA 5,6 . How these highly conserved proteins fulfil such an array of different functions has been a long-standing question.Research has now started to illuminate the molecular basis for this functional diversity. In this Review, we summarize how structural data, together with biochemical and biophysical studies, have revealed unexpected modes by which these proteins function. We also discuss how novel molecular and cell biological approaches have better defined the cellular roles of DEAD box helicases. We outline our current view on common structural and mechan istic themes that have emerged, and on physical models of how these 'unusual' RNA helicases work.Structures of DEAD box RNA helicases A number of structural studies have universally shown that members of the DEAD box family contain a highly conserved helicase core that harbours the binding sites for ATP and RNA 3,4,8 . The core is surrounded by variable auxiliary domains, which are thought to be critical for the diverse functions of these enzymes.Structure of the helicase core. DEAD box proteins belong to helicase superfamily 2 (SF2) 2 . Similarly to all SF2 helicases, DEAD box proteins are built around a highly conserved helicase core of two virtually identical domains that resemble the bacterial recombination protein recombinase A (RecA) 3,4,8 (FIG. 2a,b). Within this helicase core, at least 12 characteristic sequence motifs are located at conserved positions (FIG. 2a,b). Some of these motifs are conserved across the entire SF2 family, whereas others are found only in the DEAD box family 3 ....

show abstract

Mitochondrial helicase Irc3 translocates along double‐stranded DNA

et al. 2017

View full text Add to dashboard Cite

Irc3 is a superfamily II helicase required for mitochondrial DNA stability in Saccharomyces cerevisiae. Irc3 remodels branched DNA structures, including substrates without extensive single-stranded regions. Therefore, it is unlikely that Irc3 uses the conventional single-stranded DNA translocase mechanism utilized by most helicases. Here, we demonstrate that Irc3 disrupts partially triple-stranded DNA structures in an ATP-dependent manner. Our kinetic experiments indicate that the rate of ATP hydrolysis by Irc3 is dependent on the length of the double-stranded DNA cosubstrate. Furthermore, the previously uncharacterized C-terminal region of Irc3 is essential for these two characteristic features and forms a high affinity complex with branched DNA. Together, our experiments demonstrate that Irc3 has double-stranded DNA translocase activity.

show abstract

Structure and Mechanism of Helicases and Nucleic Acid Translocases

Cited by 1,155 publications

References 122 publications

Chromatin remodeling: insights and intrigue from single-molecule studies

Chromatin remodeling: insights and intrigue from single-molecule studies

From unwinding to clamping — the DEAD box RNA helicase family

Mitochondrial helicase Irc3 translocates along double‐stranded DNA

Contact Info

Product

Resources

About