6S3M

Crystal structure of helicase Pif1 from Thermus oshimai in complex with ssDNA (dT)18 and ADP-AlF4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.

Dai, Y.X.Chen, W.F.Liu, N.N.Teng, F.Y.Guo, H.L.Hou, X.M.Dou, S.X.Rety, S.Xi, X.G.

(2021) Nucleic Acids Res 49: 4129-4143

  • DOI: 10.1093/nar/gkab188
  • Primary Citation of Related Structures:  
    6XZT, 7BIL, 7ADA, 6S3O, 6S3N, 6S3P, 6S3I, 6S3H, 6S3M, 6S3E

  • PubMed Abstract: 
  • Pif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial duplex or single-stranded DNA ...

    Pif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial duplex or single-stranded DNA. In the apo state and in complex with a partial duplex DNA, ToPif1 is monomeric with its domain 2B/loop3 adopting a closed and an open conformation, respectively. When complexed with a single-stranded DNA, ToPif1 forms a stable dimer with domain 2B/loop3 shifting to a more open conformation. Single-molecule and biochemical assays show that domain 2B/loop3 switches repetitively between the closed and open conformations when a ToPif1 monomer unwinds DNA and, in contrast with other typical dimeric SF1A helicases, dimerization has an inhibitory effect on its helicase activity. This mechanism is not general for all Pif1 helicases but illustrates the diversity of regulation mechanisms among different helicases. It also raises the possibility that although dimerization results in activation for SF1A helicases, it may lead to inhibition for some of the other uncharacterized SF1B helicases, an interesting subject warranting further studies.


    Organizational Affiliation

    Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D'Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PIF1 helicaseA, B444Thermus oshimaiMutation(s): 0 
Gene Names: Theos_1468
Find proteins for K7RJ88 (Thermus oshimai JL-2)
Explore K7RJ88 
Go to UniProtKB:  K7RJ88
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*TP*TP*TP*TP*G)-3')C, D18Thermus oshimai
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download Ideal Coordinates CCD File 
    E [auth A], H [auth B]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    ALF
    Query on ALF

    Download Ideal Coordinates CCD File 
    G [auth A], J [auth B]TETRAFLUOROALUMINATE ION
    Al F4
    UYOMQIYKOOHAMK-UHFFFAOYSA-J
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    F [auth A], I [auth B]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.11 Å
    • R-Value Free: 0.268 
    • R-Value Work: 0.224 
    • R-Value Observed: 0.226 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 87.735α = 90
    b = 101.974β = 90
    c = 250.925γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    Aimlessdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Natural Science Foundation of ChinaChina31370798,11304252,11574252,31301632

    Revision History  (Full details and data files)

    • Version 1.0: 2021-01-13
      Type: Initial release
    • Version 1.1: 2021-04-07
      Changes: Database references
    • Version 1.2: 2021-04-28
      Changes: Database references