3GXV

Three-dimensional structure of N-terminal domain of DnaB Helicase from Helicobacter pylori and its interactions with primase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Three-dimensional structure of N-terminal domain of DnaB helicase and helicase-primase interactions in Helicobacter pylori

Kashav, T.Nitharwal, R.Abdulrehman, S.A.Gabdoulkhakov, A.Saenger, W.Dhar, S.K.Gourinath, S.

(2009) PLoS One 4: e7515-e7515

  • DOI: 10.1371/journal.pone.0007515
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Replication initiation is a crucial step in genome duplication and homohexameric DnaB helicase plays a central role in the replication initiation process by unwinding the duplex DNA and interacting with several other proteins during the process of re ...

    Replication initiation is a crucial step in genome duplication and homohexameric DnaB helicase plays a central role in the replication initiation process by unwinding the duplex DNA and interacting with several other proteins during the process of replication. N-terminal domain of DnaB is critical for helicase activity and for DnaG primase interactions. We present here the crystal structure of the N-terminal domain (NTD) of H. pylori DnaB (HpDnaB) helicase at 2.2 A resolution and compare the structural differences among helicases and correlate with the functional differences. The structural details of NTD suggest that the linker region between NTD and C-terminal helicase domain plays a vital role in accurate assembly of NTD dimers. The sequence analysis of the linker regions from several helicases reveals that they should form four helix bundles. We also report the characterization of H. pylori DnaG primase and study the helicase-primase interactions, where HpDnaG primase stimulates DNA unwinding activity of HpDnaB suggesting presence of helicase-primase cohort at the replication fork. The protein-protein interaction study of C-terminal domain of primase and different deletion constructs of helicase suggests that linker is essential for proper conformation of NTD to interact strongly with HpDnaG. The surface charge distribution on the primase binding surface of NTDs of various helicases suggests that DnaB-DnaG interaction and stability of the complex is most probably charge dependent. Structure of the linker and helicase-primase interactions indicate that HpDnaB differs greatly from E.coli DnaB despite both belong to gram negative bacteria.


    Organizational Affiliation

    School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicative DNA helicase
A, B
123Helicobacter pyloriMutation(s): 0 
Gene Names: HP_1362
EC: 3.6.1 (PDB Primary Data), 3.6.4.12 (UniProt)
Find proteins for O25916 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25916

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Replicative DNA helicase
C
22Helicobacter pyloriMutation(s): 0 
Gene Names: HP_1362
EC: 3.6.1 (PDB Primary Data), 3.6.4.12 (UniProt)
Find proteins for O25916 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25916

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Replicative DNA helicase
D
26Helicobacter pyloriMutation(s): 0 
Gene Names: HP_1362
EC: 3.6.1 (PDB Primary Data), 3.6.4.12 (UniProt)
Find proteins for O25916 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25916
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.83α = 90
b = 78.15β = 90
c = 108γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
AUTOMARdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance