3R8F

Replication initiator DnaA bound to AMPPCP and single-stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.366 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


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

  • 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 cellu ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chromosomal replication initiator protein dnaA
A, B, C, D
324Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: dnaA
Find proteins for O66659 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66659
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'E12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ACP
Query on ACP

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.366 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.797α = 90.00
b = 114.219β = 90.00
c = 201.266γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
Blu-Icedata collection
PHENIXrefinement
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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