1. Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase
- Author
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Shuo-Xing Dou, Wen-Qiang Wu, Xu-Guang Xi, Wei-Fei Chen, Dan Li, Hai-Yun Ma, Na-Nv Liu, Ke-Yu Lu, Yang-Xue Dai, Stéphane Réty, Northwest A and F University, Laboratoire de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Chinese Academy of Sciences [Beijing] (UCAS), Beijing National Laboratory for Condensed Matter Physics and Institute of Physics (IoP/CAS), Chinese Academy of Sciences [Changchun Branch] (CAS), Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), BASICS, Shanghai Jiao Tong University [Shanghai], Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, xi, Xu-Guang, École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)
- Subjects
Protein Conformation, alpha-Helical ,0301 basic medicine ,Genome instability ,[SDV]Life Sciences [q-bio] ,Gene Expression ,Crystallography, X-Ray ,Substrate Specificity ,chemistry.chemical_compound ,Adenosine Triphosphate ,Structural Biology ,Cloning, Molecular ,DNA, Fungal ,[SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,ComputingMilieux_MISCELLANEOUS ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Hydrolysis ,Recombinant Proteins ,Molecular Docking Simulation ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,Biochemistry ,Thermodynamics ,Protein Binding ,Saccharomyces cerevisiae Proteins ,[SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Saccharomyces cerevisiae ,DNA, Single-Stranded ,Molecular Dynamics Simulation ,Biology ,03 medical and health sciences ,Hydrolase ,Escherichia coli ,Genetics ,Protein Interaction Domains and Motifs ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Amino Acid Sequence ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Binding site ,Binding Sites ,Sequence Homology, Amino Acid ,DNA Helicases ,Helicase ,Ribosomal RNA ,biology.organism_classification ,G-Quadruplexes ,DNA binding site ,Kinetics ,030104 developmental biology ,chemistry ,biology.protein ,Protein Conformation, beta-Strand ,Protein Multimerization ,Sequence Alignment ,DNA - Abstract
International audience; The Saccharomyces cerevisiae Pif1 protein (ScPif1p) is the prototypical member of the Pif1 family of DNA helicases. ScPif1p is involved in the maintenance of mitochondrial, ribosomal and telomeric DNA and suppresses genome instability at G-quadruplex motifs. Here, we report the crystal structures of a truncated ScPif1p (ScPif1p237−780) in complex with different ssDNAs. Our results have revealed that a yeast-specific insertion domain protruding from the 2B domain folds as a bundle bearing an α-helix, α16. The α16 helix regulates the helicase activities of ScPif1p through interactions with the previously identified loop3. Furthermore, a biologically relevant dimeric structure has been identified, which can be further specifically stabilized by G-quadruplex DNA. Basing on structural analyses and mutational studies with DNA binding and unwinding assays, a potential G-quadruplex DNA binding site in ScPif1p monomers is suggested. Our results also show that ScPif1p uses the Q-motif to preferentially hydrolyze ATP, and a G-rich tract is preferentially recognized by more residues, consistent with previous biochemical observations. These findings provide a structural and mechanistic basis for understanding the multifunctional ScPif1p.
- Published
- 2017