title: Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1.
abstract: Pif1 is a conserved SF1B DNA helicase involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. Here, we report the structures of the helicase domain of human Pif1 and Bacteroides sp Pif1 (BaPif1) in complex with ADP-AlF4(-) and two different single-stranded DNAs (ssDNAs). The wedge region equivalent to the β hairpin in other SF1B DNA helicases folds into an extended loop followed by an α helix. The Pif1 signature motif of BaPif1 interacts with the wedge region and a short helix in order to stabilize these ssDNA binding elements, therefore indirectly exerting its functional role. Domain 2B of BaPif1 undergoes a large conformational change upon concomitant binding of ATP and ssDNA, which is critical for Pif1's activities. BaPif1 cocrystallized with a tailed dsDNA and ADP-AlF4(-), resulting in a bound ssDNA bent nearly 90° at the ssDNA/dsDNA junction. The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity of Pif1.
authors.affiliation: Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.
authors.forename: Xianglian
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.
authors.forename: Wendan
authors.initials: W
authors.lastname: Ren
authors.affiliation: Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.
authors.forename: Sakshibeedu R
authors.initials: SR
authors.lastname: Bharath
authors.affiliation: Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.
authors.forename: Xuhua
authors.initials: X
authors.lastname: Tang
authors.affiliation: Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: He
authors.affiliation: Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.affiliation: Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China.
authors.forename: Dewang
authors.initials: D
authors.lastname: Li
authors.affiliation: Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore. Electronic address: haiwei@imcb.a-star.edu.sg.
authors.forename: Haiwei
authors.initials: H
authors.lastname: Song
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry* / Q000235:genetics; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001439:Bacteroides / Q000737:chemistry* / Q000201:enzymology; D003001:Cloning, Molecular; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004265:DNA Helicases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D054856:G-Quadruplexes; D015870:Gene Expression; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D000072417:Protein Domains; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D020033:Protein Isoforms; D011994:Recombinant Proteins; D000255:Adenosine Triphosphate; D004247:DNA; D004265:DNA Helicases; C508765:PIF1 protein, human
keywords: G quadruplex; Pif1 helicase; Pif1 signature motif; SF1B helicase