6L3G

Structural Basis for DNA Unwinding at Forked dsDNA by two coordinating Pif1 helicases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases.

Su, N.Byrd, A.K.Bharath, S.R.Yang, O.Jia, Y.Tang, X.Ha, T.Raney, K.D.Song, H.

(2019) Nat Commun 10: 5375-5375

  • DOI: 10.1038/s41467-019-13414-9

  • PubMed Abstract: 
  • Pif1 plays multiple roles in maintaining genome stability and preferentially unwinds forked dsDNA, but the mechanism by which Pif1 unwinds forked dsDNA remains elusive. Here we report the structure of Bacteroides sp Pif1 (BaPif1) in complex with a sy ...

    Pif1 plays multiple roles in maintaining genome stability and preferentially unwinds forked dsDNA, but the mechanism by which Pif1 unwinds forked dsDNA remains elusive. Here we report the structure of Bacteroides sp Pif1 (BaPif1) in complex with a symmetrical double forked dsDNA. Two interacting BaPif1 molecules are bound to each fork of the partially unwound dsDNA, and interact with the 5' arm and 3' ss/dsDNA respectively. Each of the two BaPif1 molecules is an active helicase and their interaction may regulate their helicase activities. The binding of BaPif1 to the 5' arm causes a sharp bend in the 5' ss/dsDNA junction, consequently breaking the first base-pair. BaPif1 bound to the 3' ss/dsDNA junction impacts duplex unwinding by stabilizing the unpaired first base-pair and engaging the second base-pair poised for breaking. Our results provide an unprecedented insight into how two BaPif1 coordinate with each other to unwind the forked dsDNA.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA. raneykevind@uams.edu.,Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore. haiwei@imcb.a-star.edu.sg.,Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, 310058, China. haiwei@imcb.a-star.edu.sg.,Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, 310058, China.,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore. haiwei@imcb.a-star.edu.sg.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725N. Wolfe Street, Baltimore, MD, 21205, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725N. Wolfe Street, Baltimore, MD, 21205, USA. tjha@jhu.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent DNA helicase
A, B
433Bacteroides sp. AF32-8BHMutation(s): 0 
Find proteins for A0A373G551 (Bacteroides sp. AF32-8BH)
Go to UniProtKB:  A0A373G551
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)-3')D30Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download SDF File 
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: 3.3 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.244 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 131.265α = 90.00
b = 131.265β = 90.00
c = 117.183γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Aimlessdata scaling
XFITdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670820
National Institutes of Health/National Human Genome Research InstituteUnited StatesR35GM122601

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release