PMC:4103454 / 19090-22783 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4103454","sourcedb":"PMC","sourceid":"4103454","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4103454","text":"Discussion\nFrom the evidence presented above, it is clear that, at least in bacteria and bacteriophage, VRR-Nuc domains resemble Holliday-junction-resolving enzymes both structurally and functionally. The role of these domains in bacteriophage is unknown, but analogy with systems such as λ Rep, T7 endonuclease I, or T4 endonuclease VII suggests that they may be involved in DNA recombination, replication, and/or packaging (Sharples et al., 2004, White et al., 1997). As dimers, bacterial VRR-Nuc domains have two active sites and a DNA-binding surface with 2-fold symmetry that are well suited to the recognition and symmetrical, bilateral cleavage of Holliday junctions (Déclais and Lilley, 2008). In contrast, we now show that FAN1 proteins are monomeric, consistent with a different mode of asymmetric substrate selectivity. From our models, the presence of a highly conserved helical insertion between β1 and β2 suggests two direct effects on FAN1 VRR-Nuc domain function. First, the insertion occludes dimer formation by packing against the hydrophobic face of the central core β sheet. Second, the insertion alters the shape of the DNA-binding surface and provides a significant contribution to its overall positive charge, thereby influencing substrate preference. It is highly probable that these data explain why FAN1 cannot cleave Holliday junctions and instead prefers simple branched DNA species such as 5′ flaps.\nFunctional redundancy is a characteristic of DNA repair pathways with multiple structure-specific enzymes sharing common substrates and/or activities that are controlled by regulatory factors. For example, FAN1 and FEN1 share both 5′ flap endonuclease and 5′-3′ exonuclease activity (Harrington and Lieber, 1994). The relationship between FAN1 and the bacterial examples of VRR-Nuc domain described above bears some comparison to the relationship of FEN1 and GEN1, another member of the Rad2/XPG family. FEN1 and GEN1 each comprise a bipartite nuclease domain and a DNA-binding helix-turn-helix domain. FEN1 preferentially targets 5′ flap structures as a monomeric enzyme. GEN1 is a monomer in solution and cleaves 5′ flaps and replication forks as a monomer but can form a dimer on Holliday junctions to ensure their productive resolution by symmetrical, bilateral cleavage (Rass et al., 2010). In this case, GEN1 possesses gain-of-function modifications to the FEN1 architecture to allow dimerization in the presence of an appropriate substrate (Tsutakawa et al., 2011). Conversely, the FAN1 VRR-Nuc domain has evolved a loss-of-function modification to prevent dimerization. Nonetheless, it is tempting to speculate that reorganization of the helical insertion, either by binding to an accessory protein or posttranslational modification, could trigger formation of FAN1 dimers. In this scenario, the hydrophobic faces of the helical insertions could pack together to form a stalk structure over the active site surface as seen in RecU, where it plays a role in HJ orientation (Cañas et al., 2011).\nAlthough FAN1 is required for ICL repair, it is not clear what step is controlled by FAN1. ICL repair involves homologous recombination (Kee and D’Andrea, 2010), and several nucleases have been identified that are thought to be responsible for resolution of the resulting Holliday junctions: SLX1 and MUS81 tethered to the SLX4 scaffold, together, and GEN1 (Castor et al., 2013, Wyatt et al., 2013). From this point of view, there is no need to invoke another resolvase activity. However, we cannot exclude the possibility that, under certain circumstances, FAN1 could be modified in a way that would enable dimerization and HJ cleavage by this nuclease in vivo.","divisions":[{"label":"Title","span":{"begin":0,"end":10}}],"tracks":[{"project":"2_test","denotations":[{"id":"24981866-15223317-20021745","span":{"begin":443,"end":447},"obj":"15223317"},{"id":"24981866-9223630-20021746","span":{"begin":463,"end":467},"obj":"9223630"},{"id":"24981866-18160275-20021747","span":{"begin":695,"end":699},"obj":"18160275"},{"id":"24981866-8131753-20021748","span":{"begin":1736,"end":1740},"obj":"8131753"},{"id":"24981866-20634321-20021749","span":{"begin":2318,"end":2322},"obj":"20634321"},{"id":"24981866-21496641-20021750","span":{"begin":2495,"end":2499},"obj":"21496641"},{"id":"24981866-21600217-20021751","span":{"begin":3024,"end":3028},"obj":"21600217"},{"id":"24981866-20713514-20021752","span":{"begin":3186,"end":3190},"obj":"20713514"},{"id":"24981866-24076219-20021753","span":{"begin":3404,"end":3408},"obj":"24076219"},{"id":"24981866-24076221-20021754","span":{"begin":3424,"end":3428},"obj":"24076221"}],"attributes":[{"subj":"24981866-15223317-20021745","pred":"source","obj":"2_test"},{"subj":"24981866-9223630-20021746","pred":"source","obj":"2_test"},{"subj":"24981866-18160275-20021747","pred":"source","obj":"2_test"},{"subj":"24981866-8131753-20021748","pred":"source","obj":"2_test"},{"subj":"24981866-20634321-20021749","pred":"source","obj":"2_test"},{"subj":"24981866-21496641-20021750","pred":"source","obj":"2_test"},{"subj":"24981866-21600217-20021751","pred":"source","obj":"2_test"},{"subj":"24981866-20713514-20021752","pred":"source","obj":"2_test"},{"subj":"24981866-24076219-20021753","pred":"source","obj":"2_test"},{"subj":"24981866-24076221-20021754","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#c3ec93","default":true}]}]}}