5O6B

Structure of ScPif1 in complex with GGGTTTT and ADP-AlF4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 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.


Macromolecules

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
EC: 3.6.4.12
UniProt
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
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*GP*TP*TP*T)-3')
C, D
8Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / 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
ALF
Query on ALF

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
PO4
Query on PO4

Download Ideal Coordinates CCD File 
K [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.246α = 90
b = 88.373β = 90
c = 187.703γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina11574252, 31370798
Northwest A &F University Startup FundingChinaZ101021103
International Associated Laboratory Helicase-mediated G-quadruplex DNA unwinding and Genome StabilityFrance--

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: 2024-05-08
    Changes: Data collection, Database references, Derived calculations