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Tatsuya Nishino

Publications and source records attributed to Tatsuya Nishino.

9 recordsLinked to original sources
PubMed2006

Cohesin's ATPase activity is stimulated by the C-terminal Winged-Helix domain of its kleisin subunit.

BACKGROUND: Cohesin, a multisubunit protein complex conserved from yeast to humans, holds sister chromatids together from the onset of replication to their separation during anaphase. Cohesin consists of four core subunits, namely Smc1, Smc3, Scc1, and Scc3. Smc1 and Smc3 proteins are characterized by 50-nm-long anti-parallel coiled coils flanked by a globular hinge domain and an ABC-like ATPase head domain. Whereas Smc1 and Smc3 heterodimerize via their hinge domains, the kleisin subunit Scc1 connects their ATPase heads, and this results in the formation of a large ring. Biochemical studies suggest that cohesin might trap sister chromatids within its ring, and genetic evidence suggests that ATP hydrolysis is required for the stable association of cohesin with chromosomes. However, the precise role of the ATPase domains remains enigmatic. RESULTS: Characterization of cohesin's ATPase activity suggests that hydrolysis depends on the binding of ATP to both Smc1 and Smc3 heads. However, ATP hydrolysis at the two active sites is not per se cooperative. We show that the C-terminal winged-helix domain of Scc1 stimulates the ATPase activity of the Smc1/Smc3 heterodimer by promoting ATP binding to Smc1's head. In contrast, we do not detect any effect of Scc1's N-terminal domain on Smc1/Smc3 ATPase activity. CONCLUSIONS: Our studies reveal that Scc1 not only connects the Smc1 and Smc3 ATPase heads but also regulates their ATPase activity.

Adenosine Triphosphate↗
PubMed2006

Structure-specific DNA nucleases: structural basis for 3D-scissors.

Structure-specific DNA nucleases play important roles in various DNA transactions such as DNA replication, repair and recombination. These enzymes recognize loops and branched DNA structures. Recent structural studies have provided detailed insights into the functions of these enzymes. Structures of Holliday junction resolvase revealed that nucleases are broadly diverged in the way in which they fold, however, are required to form homodimers with large basic patches of protein surfaces, which are complementary to DNA tertiary structures. Many nucleases maintain structure-specific recognition modes, which involve particular domain arrangements through conformal changes of flexible loops or have a separate DNA binding domain. Nucleases, such as FEN-1 and archaeal XPF, are bound to proliferating cell nuclear antigen through a common motif, and thereby actualize their inherent activities.

Archaea↗
PubMed2005

Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing.

DNA and RNA frequently form various branched intermediates that are important for the transmission of genetic information. Helicases play pivotal roles in the processing of these transient intermediates during nucleic acid metabolism. The archaeal Hef helicase/ nuclease is a representative protein that processes flap- or fork-DNA structures, and, intriguingly, its C-terminal half belongs to the XPF/Mus81 nuclease family. Here, we report the crystal structure of the helicase domain of the Hef protein from Pyrococcus furiosus. The structure reveals a novel helical insertion between the two conserved helicase core domains. This positively charged extra region, structurally similar to the "thumb" domain of DNA polymerase, plays critical roles in fork recognition. The Hef helicase/nuclease exhibits sequence similarity to the Mph1 helicase from Saccharomyces cerevisiae; XPF/Rad1, involved in DNA repair; and a putative Hef homolog identified in mammals. Hence, our findings provide a structural basis for the functional mechanisms of this helicase/nuclease family.

Adenosine Triphosphatases↗
PubMed2005

Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: asymmetric DNA binding and cleavage mechanisms.

XPF/Rad1/Mus81/Hef proteins recognize and cleave branched DNA structures. XPF and Rad1 proteins cleave the 5' side of nucleotide excision repair bubble, while Mus81 and Hef cleave similar sites of the nicked Holliday junction, fork, or flap structure. These proteins all function as dimers and consist of catalytic and helix-hairpin-helix DNA binding (HhH) domains. We have determined the crystal structure of the HhH domain of Pyrococcus furiosus Hef nuclease (HefHhH), which revealed the distinct mode of protein dimerization. Our structural and biochemical analyses also showed that each of the catalytic and HhH domains binds to distinct regions within the fork-structured DNA: each HhH domain from two separate subunits asymmetrically binds to the arm region, while the catalytic domain binds near the junction center. Upon binding to DNA, Hef nuclease disrupts base pairs near the cleavage site. It is most likely that this bipartite binding mode is conserved in the XPF/Rad1/Mus81 nuclease family.

Amino Acid Sequence↗
PubMed2004

Structure and stability of cohesin's Smc1-kleisin interaction.

A multisubunit complex called cohesin forms a huge ring structure that mediates sister chromatid cohesion, possibly by entrapping sister DNAs following replication. Cohesin's kleisin subunit Scc1 completes the ring, connecting the ABC-like ATPase heads of a V-shaped Smc1/3 heterodimer. Proteolytic cleavage of Scc1 by separase triggers sister chromatid disjunction, presumably by breaking the Scc1 bridge. One half of the SMC-kleisin bridge is revealed here by a crystal structure of Smc1's ATPase complexed with Scc1's C-terminal domain. The latter forms a winged helix that binds a pair of beta strands in Smc1's ATPase head. Mutation of conserved residues within the contact interface destroys Scc1's interaction with Smc1/3 heterodimers and eliminates cohesin function. Interaction of Scc1's N terminus with Smc3 depends on prior C terminus connection with Smc1. There is little or no turnover of Smc1-Scc1 interactions within cohesin complexes in vivo because expression of noncleavable Scc1 after DNA replication does not hinder anaphase.

Adenosine Triphosphatases↗
PubMed2003

X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease: similarity between its endonuclease domain and restriction enzymes.

The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. Here, we report the domain organization of an archaeal homolog (Hef) of this family and the X-ray crystal structure of the middle domain, with the nuclease activity. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases, including the correspondence of the GDX(n)ERKX(3)D signature motif in Hef to the PDX(n)(E/D)XK motif in restriction enzymes. This structural study also suggests that the XPF/Rad1/Mus81/ERCC1 proteins form a dimer through each interface of the nuclease domain and the helix-hairpin-helix domain. Simultaneous disruptions of both interfaces result in their dissociation into separate monomers, with strikingly reduced endonuclease activities.

Amino Acid Sequence↗
PubMed2002

Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors.

DNA nucleases catalyze the cleavage of phosphodiester bonds. These enzymes play crucial roles in various DNA repair processes, which involve DNA replication, base excision repair, nucleotide excision repair, mismatch repair, and double strand break repair. In recent years, new nucleases involved in various DNA repair processes have been reported, including the Mus81 : Mms4 (Eme1) complex, which functions during the meiotic phase and the Artemis : DNA-PK complex, which processes a V(D)J recombination intermediate. Defects of these nucleases cause genetic instability or severe immunodeficiency. Thus, structural biology on various nuclease actions is essential for the elucidation of the molecular mechanism of complex DNA repair machinery. Three-dimensional structural information of nucleases is also rapidly accumulating, thus providing important insights into the molecular architectures, as well as the DNA recognition and cleavage mechanisms. This review focuses on the three-dimensional structure-function relationships of nucleases crucial for DNA repair processes.

Animals↗