3R8F

Replication initiator DnaA bound to AMPPCP and single-stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

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This is version 1.4 of the entry. See complete history


Literature

DNA stretching by bacterial initiators promotes replication origin opening.

Duderstadt, K.E.Chuang, K.Berger, J.M.

(2011) Nature 478: 209-213

  • DOI: 10.1038/nature10455
  • Primary Citation of Related Structures:  
    3R8F

  • PubMed Abstract: 
  • Many replication initiators form higher-order oligomers that process host replication origins to promote replisome formation. In addition to dedicated duplex-DNA-binding domains, cellular initiators possess AAA+ (ATPases associated with various cellular activities) elements that drive functions ranging from protein assembly to origin recognition ...

    Many replication initiators form higher-order oligomers that process host replication origins to promote replisome formation. In addition to dedicated duplex-DNA-binding domains, cellular initiators possess AAA+ (ATPases associated with various cellular activities) elements that drive functions ranging from protein assembly to origin recognition. In bacteria, the AAA+ domain of the initiator DnaA has been proposed to assist in single-stranded DNA formation during origin melting. Here we show crystallographically and in solution that the ATP-dependent assembly of Aquifex aeolicus DnaA into a spiral oligomer creates a continuous surface that allows successive AAA+ domains to bind and extend single-stranded DNA segments. The mechanism of binding is unexpectedly similar to that of RecA, a homologous recombination factor, but it differs in that DnaA promotes a nucleic acid conformation that prevents pairing of a complementary strand. These findings, combined with strand-displacement assays, indicate that DnaA opens replication origins by a direct ATP-dependent stretching mechanism. Comparative studies reveal notable commonalities between the approach used by DnaA to engage DNA substrates and other, nucleic-acid-dependent, AAA+ systems.


    Organizational Affiliation

    Biophysics Graduate Group, University of California, Berkeley, Berkeley, California 94720, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosomal replication initiator protein dnaAA, B, C, D324Aquifex aeolicusMutation(s): 0 
Gene Names: aq_322dnaA
UniProt
Find proteins for O66659 (Aquifex aeolicus (strain VF5))
Explore O66659 
Go to UniProtKB:  O66659
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66659
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'E 12N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.797α = 90
b = 114.219β = 90
c = 201.266γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Database references
  • Version 1.2: 2012-02-22
    Changes: Non-polymer description, Refinement description
  • Version 1.3: 2012-03-28
    Changes: Database references
  • Version 1.4: 2015-09-09
    Changes: Structure summary