2WP0 | pdb_00002wp0

Crystal structure of a HobA-DnaA (domain I-II) complex from Helicobacter pylori.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.266 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.226 (Depositor) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2WP0

This is version 1.4 of the entry. See complete history

Literature

The Structure of a Dnaa/Hoba Complex from Helicobacter Pylori Provides Insight Into Regulation of DNA Replication in Bacteria.

Natrajan, G.Noirot-Gros, M.F.Zawilak-Pawlik, A.Kapp, U.Terradot, L.

(2009) Proc Natl Acad Sci U S A 106: 21115

  • DOI: https://doi.org/10.1073/pnas.0908966106
  • Primary Citation Related Structures: 
    2WP0

  • PubMed Abstract: 

    Bacterial DNA replication requires DnaA, an AAA+ ATPase that initiates replication at a specific chromosome region, oriC, and is regulated by species-specific regulators that directly bind DnaA. HobA is a DnaA binding protein, recently identified as an essential regulator of DNA replication in Helicobacter pylori. We report the crystal structure of HobA in complex with domains I and II of DnaA (DnaA(I-II)) from H. pylori, the first structure of DnaA bound to one of its regulators. Biochemical characterization of the complex formed shows that a tetramer of HobA binds four DnaA(I-II) molecules, and that DnaA(I-II) is unable to oligomerize by itself. Mutagenesis and protein-protein interaction studies demonstrate that some of the residues located at the HobA-DnaA(I-II) interface in the structure are necessary for complex formation. Introduction of selected mutations into H. pylori shows that the disruption of the interaction between HobA and DnaA is lethal for the bacteria. Remarkably, the DnaA binding site of HobA is conserved in DiaA from Escherichia coli, suggesting that the structure of the HobA/DnaA complex represents a model for DnaA regulation in other Gram-negative bacteria. Our data, together with those from other studies, indicate that HobA could play a crucial scaffolding role during the initiation of replication in H. pylori by organizing the first step of DnaA oligomerization and attachment to oriC.


  • Organizational Affiliation
    • Macromolecular Crystallography Group ESRF, 6 rue Jules Horowitz, 38043 Grenoble cedex, France.

Macromolecule Content 

  • Total Structure Weight: 68.05 kDa 
  • Atom Count: 4,479 
  • Modeled Residue Count: 532 
  • Deposited Residue Count: 584 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HOBA
A, B
180Helicobacter pyloriMutation(s): 0 
UniProt
Find proteins for O25828 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25828 
Go to UniProtKB:  O25828
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25828
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
C, D
112Helicobacter pyloriMutation(s): 0 
UniProt
Find proteins for O26057 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O26057 
Go to UniProtKB:  O26057
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26057
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
X [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]
G [auth A]
K [auth A]
L [auth B]
P [auth B]
E [auth A],
G [auth A],
K [auth A],
L [auth B],
P [auth B],
U [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
M [auth B]
O [auth B]
H [auth A],
I [auth A],
J [auth A],
M [auth B],
O [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
V [auth B],
W [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.266 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.226 (Depositor) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.56α = 90
b = 55.5β = 97.55
c = 96.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Derived calculations
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description