Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 290.86 kDa 
• Atom Count: 19058 
• Residue Count: 2281 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

3U4Q

Structure of AddAB-DNA complex at 2.8 angstroms

• DOI: 10.2210/pdb3U4Q/pdb
• NDB: NA1327

• Classification: HYDROLASE/DNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-10-10 Released: 2012-03-21 
• Deposition Author(s): Saikrishnan, K., Krajewski, W., Wigley, D.

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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 

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

• PubMed: 22307084 
• DOI: 10.1038/emboj.2012.9
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ATP-dependent helicase/nuclease subunit A	A	1232	Bacillus subtilis	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ATP-dependent helicase/deoxyribonuclease subunit B	B	1166	Bacillus subtilis	Mutation(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

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (27-MER)	X	48	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	X	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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 = 100.555	α = 90
b = 139.714	β = 105.54
c = 103.093	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-10 
• Released Date: 2012-03-21 
Deposition Author(s): Saikrishnan, K., Krajewski, W., Wigley, D.

Revision History 

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references