5FTC

Crystal structure of Pif1 helicase from Bacteroides in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.269 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of the Bspif1 Helicase Reveal that a Major Movement of the 2B SH3 Domain is Required for DNA Unwinding

Chen, W.-F.Dai, Y.-X.Duan, X.-L.Liu, N.-N.Shi, W.Li, N.Li, M.Dou, S.-X.Dong, Y.-H.Rety, S.Xi, X.-G.

(2016) Nucleic Acids Res. 44: 2949

  • DOI: 10.1093/nar/gkw033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pif1 helicases are ubiquitous members of the SF1B family and are essential for maintaining genome stability. It was speculated that Pif1-specific motifs may fold in specific structures, conferring distinct activities upon it. Here, we report the crys ...

    Pif1 helicases are ubiquitous members of the SF1B family and are essential for maintaining genome stability. It was speculated that Pif1-specific motifs may fold in specific structures, conferring distinct activities upon it. Here, we report the crystal structures of the Pif1 helicase from Bacteroides spp with and without adenosine triphosphate (ATP) analog/ssDNA. BsPif1 shares structural similarities with RecD2 and Dda helicases but has specific features in the 1B and 2B domains. The highly conserved Pif1 family specific sequence motif interacts with and constraints a putative pin-loop in domain 1B in a precise conformation. More importantly, we found that the 2B domain which contains a specific extended hairpin undergoes a significant rotation and/or movement upon ATP and DNA binding, which is absolutely required for DNA unwinding. We therefore propose a mechanism for DNA unwinding in which the 2B domain plays a predominant role. The fact that the conformational change regulates Pif1 activity may provide insight into the puzzling observation that Pif1 becomes highly processive during break-induced replication in association with PolĪ“, while the isolated Pif1 has low processivity.


    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
TPR DOMAIN PROTEIN
A
433Bacteroides sp. 3_1_23Mutation(s): 0 
Find proteins for D7K0H3 (Bacteroides sp. 3_1_23)
Go to UniProtKB:  D7K0H3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.269 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.173α = 90.00
b = 74.032β = 90.00
c = 109.153γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references
  • Version 1.2: 2016-04-20
    Type: Database references