Structure of ScPif1 in complex with polydT and ATPgS

Experimental Data Snapshot

  • Resolution: 3.28 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

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Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase.

Lu, K.Y.Chen, W.F.Rety, S.Liu, N.N.Wu, W.Q.Dai, Y.X.Li, D.Ma, H.Y.Dou, S.X.Xi, X.G.

(2018) Nucleic Acids Res 46: 1486-1500

  • DOI: https://doi.org/10.1093/nar/gkx1217
  • Primary Citation of Related Structures:  
    5O6B, 5O6D, 5O6E

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicase PIF1
A, B
545Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PIF1TST1YML061CYM9958.01C
Find proteins for P07271 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07271 
Go to UniProtKB:  P07271
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07271
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
C, D
6Saccharomyces cerevisiae
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.28 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.406α = 90
b = 90.783β = 90
c = 186.169γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description