4RKI

Crystal structure of sliding beta clamp from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into beta-Clamp and its interaction with DNA Ligase in Helicobacter pylori.

Pandey, P.Tarique, K.F.Mazumder, M.Rehman, S.A.Kumari, N.Gourinath, S.

(2016) Sci Rep 6: 31181-31181

  • DOI: 10.1038/srep31181
  • Primary Citation of Related Structures:  
  • Also Cited By: 5G4Q, 5G48

  • PubMed Abstract: 
  • Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of ...

    Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2Å structure of β-clamp from H. pylori (Hpβ-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial β-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of β-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of β-clamp binding regions in them and validated by SPR studies. Hpβ-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of β-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with β-clamp.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit beta
A
382Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: dnaN
Find proteins for O25242 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25242
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.534α = 90.00
b = 65.886β = 115.79
c = 82.723γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXmodel building
REFMACrefinement
PHENIXphasing
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references