1ZS3

The crystal structure of the Lactococcus lactis MG1363 DpsB protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structures of Lactococcus lactis MG1363 Dps proteins reveal the presence of an N-terminal helix that is required for DNA binding.

Stillman, T.J.Upadhyay, M.Norte, V.A.Sedelnikova, S.E.Carradus, M.Tzokov, S.Bullough, P.A.Shearman, C.A.Gasson, M.J.Williams, C.H.Artymiuk, P.J.Green, J.

(2005) Mol.Microbiol. 57: 1101-1112

  • DOI: 10.1111/j.1365-2958.2005.04757.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dps proteins play a major role in the protection of bacterial DNA from damage by reactive oxygen species. Previous studies have implicated the extended lysine-containing N-terminal regions of Dps subunits in DNA binding, but this part of the structur ...

    Dps proteins play a major role in the protection of bacterial DNA from damage by reactive oxygen species. Previous studies have implicated the extended lysine-containing N-terminal regions of Dps subunits in DNA binding, but this part of the structure has not previously been observed crystallographically. Here the structures of two Dps proteins (DpsA and DpsB) from Lactococcus lactis MG1363 reveal for the first time the presence of an N-terminal alpha helix that extends from the core of the Dps subunit. Consequently, the N-terminal helices are displayed in parallel pairs on the exterior of the dodecameric Dps assemblies. Both DpsA and DpsB bind DNA. Deletion of the DpsA N-terminal helix impaired DNA binding. The N-terminal Lys residues of Escherichia coli Dps have been implicated in DNA binding. Replacement of the lactococcal DpsA Lys residues 9, 15 and 16 by Glu did not inhibit DNA binding. However, DNA binding was inhibited by EDTA, suggesting a role for cations in DNA binding. In contrast to E. coli, Bacillus brevis and Mycobacterium smegmatis Dps:DNA complexes, in which DNA interacts with crystalline Dps phases, L. lactis DNA:Dps complexes appeared as non-crystalline aggregates of protein and DNA in electron micrographs.


    Related Citations: 
    • Two operons that encode FNR-like proteins in Lactococcus lactis
      Gostick, D.O.,Griffin, H.G.,Shearman, C.A.,Scott, C.,Green, J.,Gasson, M.J.,Guest, J.R.
      (1999) Mol.Microbiol. 31: 1523


    Organizational Affiliation

    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, Firth Court, Western Bank, University of Sheffield, Sheffield S10 2TN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lactococcus lactis MG1363 DpsA
A, B, C, D, E, F, G, H, I, J, K, L
182N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 127.977α = 90.00
b = 128.379β = 90.00
c = 193.903γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4phasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description