2Z4R

Crystal structure of domain III from the Thermotoga maritima replication initiation protein DnaA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Common Mechanism for the ATP-DnaA-dependent Formation of Open Complexes at the Replication Origin

Ozaki, S.Kawakami, H.Nakamura, K.Fujikawa, N.Kagawa, W.Park, S.-Y.Yokoyama, S.Kurumizaka, H.Katayama, T.

(2008) J.Biol.Chem. 283: 8351-8362

  • DOI: 10.1074/jbc.M708684200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Initiation of chromosomal replication and its cell cycle-coordinated regulation bear crucial and fundamental mechanisms in most cellular organisms. Escherichia coli DnaA protein forms a homomultimeric complex with the replication origin (oriC). ATP-D ...

    Initiation of chromosomal replication and its cell cycle-coordinated regulation bear crucial and fundamental mechanisms in most cellular organisms. Escherichia coli DnaA protein forms a homomultimeric complex with the replication origin (oriC). ATP-DnaA multimers unwind the duplex within the oriC unwinding element (DUE). In this study, structural analyses suggested that several residues exposed in the central pore of the putative structure of DnaA multimers could be important for unwinding. Using mutation analyses, we found that, of these candidate residues, DnaA Val-211 and Arg-245 are prerequisites for initiation in vivo and in vitro. Whereas DnaA V211A and R245A proteins retained normal affinities for ATP/ADP and DNA and activity for the ATP-specific conformational change of the initiation complex in vitro, oriC complexes of these mutant proteins were inactive in DUE unwinding and in binding to the single-stranded DUE. Unlike oriC complexes including ADP-DnaA or the mutant DnaA, ATP-DnaA-oriC complexes specifically bound the upper strand of single-stranded DUE. Specific T-rich sequences within the strand were required for binding. The corresponding conserved residues of the DnaA ortholog in Thermotoga maritima, an ancient eubacterium, were also required for DUE unwinding, consistent with the idea that the mechanism and regulation for DUE unwinding can be evolutionarily conserved. These findings provide novel insights into mechanisms for pore-mediated origin unwinding, ATP/ADP-dependent regulation, and helicase loading of the initiation complex.


    Organizational Affiliation

    Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chromosomal replication initiator protein dnaA
A, B, C
440Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: dnaA
Find proteins for P46798 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P46798
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADPKd: 24 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 133.335α = 90.00
b = 221.787β = 106.13
c = 55.601γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance