Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1

Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925 Barranco-Medina, 2010, DNA binding induces dimerization of Saccharomyces cerevisiae Pif1, Biochemistry, 49, 8445, 10.1021/bi100984j Bhattacharyya, 2014, Grip it and rip it: structural mechanisms of DNA helicase substrate binding and unwinding, Protein Sci., 23, 1498, 10.1002/pro.2533 Bochman, 2010, Unwinding the functions of the Pif1 family helicases, DNA Repair (Amst.), 9, 237, 10.1016/j.dnarep.2010.01.008 Bochman, 2011, The Pif1 family in prokaryotes: what are our helicases doing in your bacteria?, Mol. Biol. Cell, 22, 1955, 10.1091/mbc.E11-01-0045 Boulé, 2006, Roles of Pif1-like helicases in the maintenance of genomic stability, Nucleic Acids Res., 34, 4147, 10.1093/nar/gkl561 Boulé, 2007, The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates, Nucleic Acids Res., 35, 5809, 10.1093/nar/gkm613 Boulé, 2005, The yeast Pif1p helicase removes telomerase from telomeric DNA, Nature, 438, 57, 10.1038/nature04091 Byrd, 2015, A parallel quadruplex DNA is bound tightly but unfolded slowly by pif1 helicase, J. Biol. Chem., 290, 6482, 10.1074/jbc.M114.630749 Chib, 2016, Yeast Helicase Pif1 Unwinds RNA:DNA Hybrids with Higher Processivity than DNA:DNA Duplexes, J. Biol. Chem., 2, 2 Chisholm, 2012, A genomewide screen for suppressors of Alu-mediated rearrangements reveals a role for PIF1, PLoS ONE, 7, e30748, 10.1371/journal.pone.0030748 Emsley, 2010, Features and development of Coot, Acta Crystallogr. D Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493 Galletto, 2013, Translocation of Saccharomyces cerevisiae Pif1 helicase monomers on single-stranded DNA, Nucleic Acids Res., 41, 4613, 10.1093/nar/gkt117 George, 2009, Human Pif1 helicase unwinds synthetic DNA structures resembling stalled DNA replication forks, Nucleic Acids Res., 37, 6491, 10.1093/nar/gkp671 Gu, 2008, Biochemical analysis of human PIF1 helicase and functions of its N-terminal domain, Nucleic Acids Res., 36, 6295, 10.1093/nar/gkn609 He, 2012, The T4 phage SF1B helicase Dda is structurally optimized to perform DNA strand separation, Structure, 20, 1189, 10.1016/j.str.2012.04.013 Hou, 2015, Molecular mechanism of G-quadruplex unwinding helicase: sequential and repetitive unfolding of G-quadruplex by Pif1 helicase, Biochem. J., 466, 189, 10.1042/BJ20140997 Ivessa, 2000, The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA, Cell, 100, 479, 10.1016/S0092-8674(00)80683-2 Lahaye, 1993, PIF1 DNA helicase from Saccharomyces cerevisiae. Biochemical characterization of the enzyme, J. Biol. Chem., 268, 26155, 10.1016/S0021-9258(19)74294-X Lee, 2006, UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke, Cell, 127, 1349, 10.1016/j.cell.2006.10.049 Liu, 2015, The Bacteroides sp. 3_1_23 Pif1 protein is a multifunctional helicase, Nucleic Acids Res., 43, 8942, 10.1093/nar/gkv916 Lopes, 2011, G-quadruplex-induced instability during leading-strand replication, EMBO J., 30, 4033, 10.1038/emboj.2011.316 Manthei, 2015, Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases, Proc. Natl. Acad. Sci. USA, 112, 4292, 10.1073/pnas.1416746112 McCoy, 2007, Phaser crystallographic software, J. Appl. Cryst., 40, 658, 10.1107/S0021889807021206 Murshudov, 1997, Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr. D Biol. Crystallogr., 53, 240, 10.1107/S0907444996012255 Myung, 2001, Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae, Nature, 411, 1073, 10.1038/35082608 Paeschke, 2011, DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase, Cell, 145, 678, 10.1016/j.cell.2011.04.015 Paeschke, 2013, Pif1 family helicases suppress genome instability at G-quadruplex motifs, Nature, 497, 458, 10.1038/nature12149 Pike, 2015, Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: insights from DNA complex structures, Proc. Natl. Acad. Sci. USA, 112, 4286, 10.1073/pnas.1417594112 Ramanagoudr-Bhojappa, 2013, Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA, J. Biol. Chem., 288, 16185, 10.1074/jbc.M113.470013 Raney, 2013, Structure and Mechanisms of SF1 DNA Helicases, Adv. Exp. Med. Biol., 767, 17, 10.1007/978-1-4614-5037-5_2 Ribeyre, 2009, The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo, PLoS Genet., 5, e1000475, 10.1371/journal.pgen.1000475 Saikrishnan, 2008, DNA binding to RecD: role of the 1B domain in SF1B helicase activity, EMBO J., 27, 2222, 10.1038/emboj.2008.144 Saikrishnan, 2009, Mechanistic basis of 5′-3′ translocation in SF1B helicases, Cell, 137, 849, 10.1016/j.cell.2009.03.036 Sanders, 2010, Human Pif1 helicase is a G-quadruplex DNA-binding protein with G-quadruplex DNA-unwinding activity, Biochem. J., 430, 119, 10.1042/BJ20100612 Schulz, 1994, The saccharomyces PIF1 DNA helicase inhibits telomere elongation and de novo telomere formation, Cell, 76, 145, 10.1016/0092-8674(94)90179-1 Sengoku, 2006, Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa, Cell, 125, 287, 10.1016/j.cell.2006.01.054 Singleton, 2007, Structure and mechanism of helicases and nucleic acid translocases, Annu. Rev. Biochem., 76, 23, 10.1146/annurev.biochem.76.052305.115300 Terwilliger, 2003, SOLVE and RESOLVE: automated structure solution and density modification, Methods Enzymol., 374, 22, 10.1016/S0076-6879(03)74002-6 Velankar, 1999, Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism, Cell, 97, 75, 10.1016/S0092-8674(00)80716-3 Wilson, 2013, Pif1 helicase and Polδ promote recombination-coupled DNA synthesis via bubble migration, Nature, 502, 393, 10.1038/nature12585 Winn, 2011, Overview of the CCP4 suite and current developments, Acta Crystallogr. D Biol. Crystallogr., 67, 235, 10.1107/S0907444910045749 Zhang, 2006, The human Pif1 helicase, a potential Escherichia coli RecD homologue, inhibits telomerase activity, Nucleic Acids Res., 34, 1393, 10.1093/nar/gkl029 Zhou, 2000, Pif1p helicase, a catalytic inhibitor of telomerase in yeast, Science, 289, 771, 10.1126/science.289.5480.771 Zhou, 2014, Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA, eLife, 3, e02190, 10.7554/eLife.02190