7ADA

Crystal structure of helicase Pif1 from Thermus oshimai mutant Q164C-E409C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


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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 

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

  • 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 helicase AB446Thermus oshimai JL-2Mutation(s): 2 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.07α = 90
b = 58.679β = 92.208
c = 118.155γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31370798,11304252,11574252,31301632

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release