Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures

Dürr, Harald; Flaus, Andrew; Owen-Hughes, Tom; Hopfner, Karl‐Peter

doi:10.1093/nar/gkl540

Cited by 102 publications

(99 citation statements)

References 94 publications

(131 reference statements)

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“…Although no structural information is available for this gap, the DNA components of the RapA-PTC assembly may include the upstream dsDNA, the coding and non-coding strands in the transcription bubble, and the downstream dsDNA. This DNA architecture mimics the bent-and-open DNA model recently proposed for the T7 RNAP (41), and the polarity of the upstream dsDNA is consistent with the unified mechanism for the Swi2/Snf2 enzymes and DEXX box helicases (42).…”

Section: Discussionsupporting

confidence: 83%

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase

Kakar

Lubkowska

Zhou

et al. 2015

Journal of Biological Chemistry

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Background: During transcription, RapA recycles RNA polymerase (RNAP) using its ATPase activity. Results: The binding mode and binding site of RapA on RNAP are characterized. Conclusion: The ATPase activity of RapA is inhibited by its N-terminal domain but stimulated by RNAP in an allosteric fashion. Significance: Conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling.

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Section: Discussionsupporting

confidence: 83%

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase

Kakar

Lubkowska

Zhou

et al. 2015

Journal of Biological Chemistry

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“…4C). The smaller protein lobe appears to correspond to the HARP domain in contact with the ssDNA or the ssDNA-dsDNA junction, which would place the larger ATPase domain in contact with the dsDNA, consistent with dsDNA translocase activity of the SNF2 superfamily (59,60). Thus, the SAXS data are consistent with a DNA-binding function of the HARP domain and a conformational change that effects how the catalytic domain engages the DNA in the presence of nucleotide.…”

Section: Resultssupporting

confidence: 55%

A structure-specific nucleic acid-binding domain conserved among DNA repair proteins

Mason

Rambo

Greer

et al. 2014

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

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SMARCAL1, a DNA remodeling protein fundamental to genome integrity during replication, is the only gene associated with the developmental disorder Schimke immuno-osseous dysplasia (SIOD). SMARCAL1-deficient cells show collapsed replication forks, S-phase cell cycle arrest, increased chromosomal breaks, hypersensitivity to genotoxic agents, and chromosomal instability. The SMARCAL1 catalytic domain (SMARCAL1 CD ) is composed of an SNF2-type doublestranded DNA motor ATPase fused to a HARP domain of unknown function. The mechanisms by which SMARCAL1 and other DNA translocases repair replication forks are poorly understood, in part because of a lack of structural information on the domains outside of the common ATPase motor. In the present work, we determined the crystal structure of the SMARCAL1 HARP domain and examined its conformation and assembly in solution by small angle X-ray scattering. We report that this domain is conserved with the DNA mismatch and damage recognition domains of MutS/MSH and NER helicase XPB, respectively, as well as with the putative DNA specificity motif of the T4 phage fork regression protein UvsW. Loss of UvsW fork regression activity by deletion of this domain was rescued by its replacement with HARP, establishing the importance of this domain in UvsW and demonstrating a functional complementarity between these structurally homologous domains. Mutation of predicted DNA-binding residues in HARP dramatically reduced fork binding and regression activities of SMARCAL1 CD . Thus, this work has uncovered a conserved substrate recognition domain in DNA repair enzymes that couples ATP-hydrolysis to remodeling of a variety of DNA structures, and provides insight into this domain's role in replication fork stability and genome integrity.replication restart | fork reversal A ccurate DNA replication is essential for genomic stability (1). Aberrant DNA structures, protein barriers, and chemically modified DNA thwart progression of the replication fork and lead to mutations, cytotoxicity, and increased chromosomal rearrangements (2-5). Uncoupling of polymerase and helicase activities at a stalled fork (6) results in an accumulation of singlestranded (ss) DNA (Fig. 1A), rendering the genome susceptible to nuclease cleavage and thereby increasing the probability of genetic rearrangements (7-9). Failure to stabilize stalled forks can lead to replisome dissociation and fork degradation or collapse. DNA damage response (DDR) pathways maintain genomic integrity by rectifying or protecting stalled or collapsed forks and regulating DNA repair (9-11). In humans, accumulation of the ssDNA-binding protein Replication Protein A (RPA) at stalled forks signals recruitment of the S-phase checkpoint kinase ATR (12-15), consequently triggering recruitment of proteins that promote sister chromatid cohesion and stabilize the histone/chromatin structure (16).Stabilization, repair, and restart of stalled forks can involve regression of the fork into a four-stranded "chicken foot" structure, in which the nascent DNA str...

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“…2 A and B). The best fit was found by moving the XPB model along the DNA, retaining the association with the minor groove, characteristic of this family of helicases (14). The crystal structure of human XPD, a human homolog of Rad3 (15), was a good match to EM density in the location identified by cross-linking for Rad3 ( Fig.…”

Section: Resultsmentioning

confidence: 88%

Structure of an RNA polymerase II preinitiation complex

Murakami

Tsai

Kalisman

et al. 2015

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

107

120

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The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription.-E, -F, and -H, are required for the initiation of RNA polymerase II (pol II) transcription. The GTFs can be assembled with pol II and promoter DNA in a preinitiation complex (PIC) capable of efficient conversion to a transcribing complex (0.1-0.3 transcripts per template). Cryo-EM of the PIC at a resolution of 15-20 Å revealed a bipartite structure, with a P-lobe containing pol II and a G-lobe containing most of the mass of the GTFs (1). A cylinder of electron density, attributed to promoter DNA, was in contact only with GTFs and not with pol II. This architecture was consistent with the pathway of assembly of the PIC, beginning with a complex of promoter DNA and all but one of the GTFs, to which a complex of pol II and the remaining GTF was added (2).A combination of chemical cross-linking and mass spectrometry was used to locate the subunits of the GTFs in the low-resolution cryo-EM electron density map of the PIC. TFIIB was in proximity to promoter DNA at the upstream end of the pol II active center cleft, whereas Ssl2, a subunit of TFIIH, was in apparent contact with promoter DNA at the downstream end of the cleft. TFIIB bridges between pol II and promoter DNA, whereas Ssl2 is a DNA helicase, responsible for unwinding promoter DNA.The association of promoter DNA with the GTFs and not with pol II may be viewed as a fundamental principle of the PIC. Doublestranded DNA is straight and relatively rigid, whereas DNA would need to bend by about 90°to bind in the pol II active center cleft. The GTFs assemble on the double-stranded DNA, position it above the active center, and unwind the DNA. The resulting singlestranded region is flexible and can bend and bind in the pol II cleft.Cryo-EM of the PIC with state-of-the-art instrumentation has resulted in an electron density map at higher resolution. The improved map has confirmed and extended the previous findings and conclusions. ResultsCryo-EM and 3D Reconstruction. A PIC was formed as described (2) on an 86-bp fragment of HIS4 promoter DNA fragment, with pol II, GTFs (TFIIA, TFIIB, TBP, TFIIE, TFIIF, and holo-TFIIH), TFIIS, and with the ad...

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Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures

Cited by 102 publications

References 94 publications

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase

A structure-specific nucleic acid-binding domain conserved among DNA repair proteins

Structure of an RNA polymerase II preinitiation complex

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