4CEH

Crystal structure of AddAB with a forked DNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites.

Krajewski, W.W.Fu, X.Wilkinson, M.Cronin, N.B.Dillingham, M.S.Wigley, D.B.

(2014) Nature 508: 416

  • DOI: 10.1038/nature13037
  • Primary Citation of Related Structures:  4CEI, 4CEJ

  • PubMed Abstract: 
  • In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ (Chi) and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease (reviewed in refs 3 ...

    In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ (Chi) and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease (reviewed in refs 3, 4). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a χ sequence, whereupon they produce a 3' single-stranded DNA tail onto which they initiate loading of the RecA protein. Consequently, regulation of the AddAB/RecBCD complex by χ is a key control point in DNA repair and other processes involving genetic recombination. Here we report crystal structures of Bacillus subtilis AddAB in complex with different χ-containing DNA substrates either with or without a non-hydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, suggests how the enzyme binds specifically to χ sequences, and explains how χ recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single-molecule experiments.


    Organizational Affiliation

    1] Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK [2] CRT Discovery Laboratories, Department of Biological Sciences, Birkbeck, University of London, London WC1E 7HX, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A
A
1232Bacillus subtilis (strain 168)Gene Names: addA
EC: 3.1.-.-, 3.6.4.12
Find proteins for P23478 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P23478
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B
B
1166Bacillus subtilis (strain 168)Gene Names: addB
EC: 3.1.-.-, 3.6.4.12
Find proteins for P23477 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P23477
Entity ID: 3
MoleculeChainsLengthOrganism
DNAX65synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 77.373α = 104.38
b = 96.766β = 96.11
c = 109.693γ = 90.03
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHENIXphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references
  • Version 1.2: 2014-04-23
    Type: Database references