Dissection of the Regional Roles of the Archaeal Holliday Junction Resolvase Hjc by Structural and Mutational Analyses

Nishino, Tatsuya; Komori, Keishi; Ishino, Yuji; Morikawa, Kosuke

doi:10.1074/jbc.m104460200

Cited by 19 publications

(23 citation statements)

References 30 publications

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“…4C). This domain is similar to that of type II restriction enzymes (Kosinski et al 2005) and single-domain VRR nuc proteins from phage or bacteria (Pennell et al 2014) and is most similar to the HJ cleavage enzyme of Pyrococcus furiosus (PfHjc [1GEF]) (Fig 2H;Nishino et al 2001). The catalytic subdomain of PaFAN1 VRR nuc and PfHjc share low sequence identity (11.5%) and 3.0 Å root mean square deviation for 69 Ca atoms (Fig.…”

Section: Specific Features Of Individual Domainsmentioning

confidence: 84%

“…In the single-domain VRR nuc or PfHjc, the central four-or fivestranded sheet is surrounded by helices on each side and interacts with the hydrophobic b sheet of the opposing molecule to form a dimer. Such a dimeric arrangement of the single-domain VRR nuc or PfHjc allows these proteins to cleave intact HJs (Nishino et al 2001;McGregor et al 2005;Pennell et al 2014). In contrast, the VRR nuc domain of FAN1 contains a six-helix bundle inserted between the second (b7) and third (b8) strand of the b sheet, at the equivalent position of an opposing molecule in the dimeric HJ resolvase (PfHjc or Bacillus subtilis RecU [1ZP7]).…”

Section: Specific Features Of Individual Domainsmentioning

confidence: 99%

“…Archaeal HJ resolvases may have adapted to integrate into the FA complex Structures of phage and bacterial single-domain VRR nucs or archaeal and bacterial HJ resolvases show that these proteins form a dimer that is essential for intact HJ cleavage (Nishino et al 2001;McGregor et al 2005;Pennell et al 2014). In PaFAN1, the six-helix bundle subdomain is fused to the catalytic subdomain and is located at the opposing monomer of the single-domain VRR nuc or archaeal Hjc.…”

Section: Fan1 Shares Several Common Features With Other Structure-selmentioning

confidence: 99%

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Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

et al. 2014

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Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of crosslinks, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI-FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 59 flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 59 flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.

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Section: Specific Features Of Individual Domainsmentioning

confidence: 84%

Section: Specific Features Of Individual Domainsmentioning

confidence: 99%

Section: Fan1 Shares Several Common Features With Other Structure-selmentioning

confidence: 99%

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Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

et al. 2014

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“…4A) (Kvaratskhelia et al 2000;Fogg et al 2001). Hjc induces a local disruption of base pairing near the point of strand exchange, which is mediated by the flexible amino-terminal segment (Kvaratskhelia et al 2000;Nishino et al 2001a). …”

Section: Hj Resolvases In Archaeamentioning

confidence: 99%

Holliday Junction Resolvases

Wyatt

West

2014

Cold Spring Harbor Perspectives in Biology

183

194

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Four-way DNA intermediates, called Holliday junctions (HJs), can form during meiotic and mitotic recombination, and their removal is crucial for chromosome segregation. A group of ubiquitous and highly specialized structure-selective endonucleases catalyze the cleavage of HJs into two disconnected DNA duplexes in a reaction called HJ resolution. These enzymes, called HJ resolvases, have been identified in bacteria and their bacteriophages, archaea, and eukaryotes. In this review, we discuss fundamental aspects of the HJ structure and their interaction with junction-resolving enzymes. This is followed by a brief discussion of the eubacterial RuvABC enzymes, which provide the paradigm for HJ resolvases in other organisms. Finally, we review the biochemical and structural properties of some well-characterized resolvases from archaea, bacteriophage, and eukaryotes.

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“…We identified an archaeal HJ resolvase, named Hjc (Komori et al, 1999). Hjc lacks sequence and three-dimensional structure similarities with any other known HJ resolvase (Komori et al, 1999;Komori et al, 2000c;Komori et al, 2000d;Daiyasu et al, 2000;Nishino et al, 2001a;Nishino et al, 2001b).…”

Section: Introductionmentioning

confidence: 99%

Novel endonuclease in Archaea cleaving DNA with various branched structure.

et al. 2002

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We identified a novel structure-specific endonuclease in Pyrococcus furiosus. This nuclease contains two distinct domains, which are similar to the DEAH helicase family at the N-terminal two-third and the XPF endonuclease superfamily at the C-terminal one-third of the protein, respectively. The C-terminal domain has an endonuclease activity cleaving the DNA strand at the 5'-side of nicked or flapped positions in the duplex DNA. The nuclease also incises in the proximity of the 5'-side of a branch point in the template strand for leading synthesis in the fork-structured DNA. The N-terminal helicase may work cooperatively to change the fork structure suitable for cleavage by the C-terminal endonuclease. This protein, designated as Hef (helicase-associated endonuclease for fork-structured DNA), may be a prototypical enzyme for resolving stalled forks during DNA replication, as well as working at nucleotide excision repair.

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Dissection of the Regional Roles of the Archaeal Holliday Junction Resolvase Hjc by Structural and Mutational Analyses

Cited by 19 publications

References 30 publications

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

Holliday Junction Resolvases

Novel endonuclease in Archaea cleaving DNA with various branched structure.

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