3U4Q

Structure of AddAB-DNA complex at 2.8 angstroms

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1038/emboj.2012.9
  • Primary Citation of Related Structures:  
    3U4Q, 3U44

  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent helicase/nuclease subunit AA1232Bacillus subtilisMutation(s): 1 
Gene Names: addA, BSU10630
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
Find proteins for P23478 (Bacillus subtilis (strain 168))
Explore P23478 
Go to UniProtKB:  P23478
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent helicase/deoxyribonuclease subunit BB1166Bacillus subtilisMutation(s): 1 
Gene Names: addB, BSU10620
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
Find proteins for P23477 (Bacillus subtilis (strain 168))
Explore P23477 
Go to UniProtKB:  P23477
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (27-MER)C [auth X]48N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
 D [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
 E [auth X]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.555α = 90
b = 139.714β = 105.54
c = 103.093γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata 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