3U44

Crystal structure of AddAB-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex.

Saikrishnan, K.Yeeles, J.T.Gilhooly, N.S.Krajewski, W.W.Dillingham, M.S.Wigley, D.B.

(2012) EMBO J 31: 1568-1578

  • DOI: https://doi.org/10.1038/emboj.2012.9
  • Primary Citation of Related Structures:  
    3U44, 3U4Q

  • PubMed Abstract: 

    In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence Chi and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease. Here, we report the crystal structure of AddAB bound to DNA. The structure allows identification of a putative Chi-recognition site in an inactivated helicase domain of the AddB subunit. By generating mutant protein complexes that do not respond to Chi, we show that residues responsible for Chi recognition are located in positions equivalent to the signature motifs of a conventional helicase. Comparison with the related RecBCD complex, which recognizes a different Chi sequence, provides further insight into the structural basis for sequence-specific ssDNA recognition. The structure suggests a simple mechanism for DNA break processing, explains how AddAB and RecBCD can accomplish the same overall reaction with different sets of functional modules and reveals details of the role of an Fe-S cluster in protein stability and DNA binding.


  • Organizational Affiliation

    Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent helicase/nuclease subunit A1,232Bacillus subtilisMutation(s): 1 
Gene Names: addABSU10630
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
UniProt
Find proteins for P23478 (Bacillus subtilis (strain 168))
Explore P23478 
Go to UniProtKB:  P23478
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23478
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent helicase/deoxyribonuclease subunit B1,166Bacillus subtilisMutation(s): 1 
Gene Names: addBBSU10620
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
UniProt
Find proteins for P23477 (Bacillus subtilis (strain 168))
Explore P23477 
Go to UniProtKB:  P23477
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23477
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (36-MER)C [auth X]48N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
D [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.23α = 90
b = 138.96β = 105.33
c = 102.97γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations