4CEJ

Crystal structure of AddAB-DNA-ADPNP complex at 3 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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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:  
    4CEH, 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, 4) ...

    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

    Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT AA1232Bacillus subtilis subsp. subtilis str. 168Mutation(s): 2 
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT BB1166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 3 
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNAC [auth X]70synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

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F [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.437α = 90
b = 152.941β = 94.3
c = 125.244γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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