5O6E

Structure of ScPif1 in complex with TTTGGGTT and ADP-AlF4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.345 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1093/nar/gkx1217
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent DNA helicase PIF1
A, B
545Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PIF1 (TST1)
EC: 3.6.4.12
Find proteins for P07271 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: PIF1
Go to UniProtKB:  P07271
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*TP*GP*GP*T)-3')C,D7Saccharomyces cerevisiae
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ALF
Query on ALF

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Download CCD File 
A, B
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.345 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 150.605α = 90.00
b = 150.605β = 90.00
c = 136.339γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Database references