Crystal structure of the Holliday junction DNA in complex with a single RuvA tetramer

Ariyoshi, Mariko; Nishino, Tatsuya; Iwasaki, Hiroshi; Shinagawa, Hideo; Morikawa, Kosuke

doi:10.1073/pnas.140212997

Cited by 123 publications

(156 citation statements)

References 31 publications

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“…This conformation may be preferable for Mus81 because it was reported that several studied junction-specific nucleases show preference for the DNA junctions in the open conformation (36). The proposed mechanism has a precedent: RuvA protein stabilizes HJs in a square-plane (open) conformation, facilitating RuvAB branch migration and, presumably, RuvC cleavage (37). Stimulation of hMus81 activity by hRad54 in vitro is consistent with genetic data because a functional link between Rad54 and Mus81 is documented.…”

Section: Discussionsupporting

confidence: 74%

Human Rad54 protein stimulates human Mus81–Eme1 endonuclease

Mazina

Mazin

2008

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

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Rad54, a key protein of homologous recombination, physically interacts with a DNA structure-specific endonuclease, Mus81-Eme1. Genetic data indicate that Mus81-Eme1 and Rad54 might function together in the repair of damaged DNA. In vitro, Rad54 promotes branch migration of Holliday junctions, whereas the Mus81-Eme1 complex resolves DNA junctions by endonucleolytic cleavage. Here, we show that human Rad54 stimulates Mus81-Eme1 endonuclease activity on various Holliday junction-like intermediates. This stimulation is the product of specific interactions between the human Rad54 (hRad54) and Mus81 proteins, considering that Saccharomyces cerevisiae Rad54 protein does not stimulate human Mus81-Eme1 endonuclease activity. Stimulation of Mus81-Eme1 cleavage activity depends on formation of specific Rad54 complexes on DNA substrates occurring in the presence of ATP and, to a smaller extent, of other nucleotide cofactors. Thus, our results demonstrate a functional link between the branch migration activity of hRad54 and the structurespecific endonuclease activity of hMus81-Eme1, suggesting that the Rad54 and Mus81-Eme1 proteins may cooperate in the processing of Holliday junction-like intermediates during homologous recombination or DNA repair.branch migration ͉ Holliday junction resolution ͉ homologous recombination H omologous recombination (HR) is responsible for the repair of DNA double-stranded breaks (DSB) and faithful chromosome segregation during meiosis (1). The Holliday junction (HJ) is a central intermediate of HR (2). HJs are thought to form during meiotic recombination, DSB repair, and repair of collapsed replication forks (3, 4). At late stages of HR or DNA repair, HJs, which constitute a physical link between DNA molecules, must be resolved to allow chromosome separation. Enzymes that cleave HJs, called HJ resolvases, are structure-specific endonucleases that introduce coordinated single-strand cuts across the junction (5). Several HJ resolvases from bacteriophages, eubacteria, archaea, eukaryotic viruses, and mitochondria have been identified, isolated, and characterized (5). However, the identity of eukaryotic nuclear HJ resolvases is still elusive.A role for Mus81 in HJ resolution was first proposed in studies on Schizosaccharomyces pombe, where Mus81 was identified as a critical factor for the production of viable spores, survival under conditions that lead to stalling of replication fork progression, and viability in the absence of RecQ helicase, Rqh1 (6). All of the defects in S. pombe mus81 mutants were rescued by expression of RusA, a bacteriophage resolvase that is highly specific for HJs (7). Mus81 protein is widely conserved among eukaryotes, including Saccharomyces cerevisiae (8), S. pombe (6), Arabidopsis thaliana (9), mice (10, 11), and humans (12). Mus81 is related to the XPF family of structure-specific endonucleases, which share a highly conserved motif (V/IERKX 3 D) that constitutes an integral part of the endonuclease catalytic site. Mus81 functions as a heterodimer with a noncatalytic p...

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Section: Discussionsupporting

confidence: 74%

Human Rad54 protein stimulates human Mus81–Eme1 endonuclease

Mazina

Mazin

2008

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

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“…The domains in ERCC1 and XPF are structurally similar to the tandem HhH 2 found in the prokaryotic proteins UvrC and RuvA [16,[36][37][38][39]. The DNA binding properties of the isolated HhH 2 domains of ERCC1 and XPF have been evaluated [16].…”

Section: Ercc1-xpf Focusmentioning

confidence: 98%

DNA repair gets physical: Mapping an XPA-binding site on ERCC1

Croteau¹,

Ye²,

Houten³

2008

DNA Repair

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Two recent reports provide new physical information on how the XPA protein recruits the ERCC1-XPF heterodimer to the site of damage during the process of mammalian nucleotide excision repair (NER). Using chemical shift perturbation NMR experiments, the contact sites between a central fragment of ERCC1 and a XPA fragment have been mapped. While both studies agree with regard to the XPA binding site, they differ on whether the ERCC1-XPA complex can simultaneously bind DNA. These studies have important implications for both the molecular process and the design of potential inhibitors of NER.

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“…Four of these amino acids are hydrophobic residues located in domain III of E. coli RuvA and are likely to form an interface with RuvB. X-ray crystallography of the E. coli RuvA-Holliday junction complex revealed that two helix-hairpin-helix (HhH) motifs in domain II are involved in Holliday junction binding (Ariyoshi et al, 2000). The nitrogens of the main chain amides of Gly-80 and Gly-82 in the hairpin in HhH I interact with phosphate oxygens of the junction DNA through hydrogen bonds.…”

Section: Resultsmentioning

confidence: 99%

“…The secondary structure of E. coli RuvA (α helices and β strands) is shown above the alignment and is indicated by arrows (β strands) and bold lines (α helices). Domains 1, 2, and 3 include β1 to β6, α2 to α6, and α7 to α9, respectively (Ariyoshi et al, 2000;Nishino et al, 1998;Rafferty et al, 1996). The striped bars between domains 2 and 3 indicate disordered structure.…”

Section: Resultsmentioning

confidence: 99%

Identification and characterization of Thermus thermophilus HB8 RuvA protein, the subunit of the RuvAB protein complex that promotes branch migration of Holliday junctions.

et al. 2000

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The Escherichia coli ruvA and ruvB genes constitute an SOS-regulated operon. The products of these genes form a protein complex that promotes branch migration of the Holliday junction, an intermediate of homologous recombination. RuvA protein binds specifically to the Holliday junction and recruits RuvB protein to the junction. RuvB is an ATP-driven motor protein involved in branch migration. We previously cloned the ruvB gene of the thermophilic bacterium Thermus thermophilus HB8 (Tth) and found that, in contrast to the operon structure in most mesothermic bacteria, the ruvA gene is absent from the vicinity of ruvB. In this work, we cloned the ruvA gene from T. thermophilus HB8 and analyzed its nucleotide sequence. Tth RuvA is a protein of 20,414 Da consisting of 191 amino acid residues, and is 37% identical in amino acid sequence to E. coli RuvA. Tth ruvA complemented the DNA repair defect of E. coli ∆ruvA mutants. The purified Tth RuvA protein stimulated Tth RuvB activities, such as hydrolysis of ATP and promotion of branch migration of the Holliday junction, in a manner similar to the RuvA-RuvB interactions observed in E. coli. In addition, Tth RuvA stimulated the E. coli RuvB activities in vitro, which was well consistent with the results of in vivo hetero-complementation experiments.

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Crystal structure of the Holliday junction DNA in complex with a single RuvA tetramer

Cited by 123 publications

References 31 publications

Human Rad54 protein stimulates human Mus81–Eme1 endonuclease

Human Rad54 protein stimulates human Mus81–Eme1 endonuclease

DNA repair gets physical: Mapping an XPA-binding site on ERCC1

Identification and characterization of Thermus thermophilus HB8 RuvA protein, the subunit of the RuvAB protein complex that promotes branch migration of Holliday junctions.

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