6OZX

Wild type GapR crystal structure 1 from C. crescentus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.851 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of GapR reveal a central channel which could accommodate B-DNA.

Tarry, M.J.Harmel, C.Taylor, J.A.Marczynski, G.T.Schmeing, T.M.

(2019) Sci Rep 9: 16679-16679

  • DOI: 10.1038/s41598-019-52964-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GapR is a nucleoid-associated protein required for the cell cycle of Caulobacter cresentus. We have determined new crystal structures of GapR to high resolution. As in a recently published structure, a GapR monomer folds into one long N-terminal α he ...

    GapR is a nucleoid-associated protein required for the cell cycle of Caulobacter cresentus. We have determined new crystal structures of GapR to high resolution. As in a recently published structure, a GapR monomer folds into one long N-terminal α helix and two shorter α helices, and assembles into a tetrameric ring with a closed, positively charged, central channel. In contrast to the conclusions drawn from the published structures, we observe that the central channel of the tetramer presented here could freely accommodate B-DNA. Mutation of six conserved lysine residues lining the cavity and electrophoretic mobility gel shift experiments confirmed their role in DNA binding and the channel as the site of DNA binding. Although present in our crystals, DNA could not be observed in the electron density maps, suggesting that DNA binding is non-specific, which could be important for tetramer-ring translocation along the chromosome. In conjunction with previous GapR structures we propose a model for DNA binding and translocation that explains key published observations on GapR and its biological functions.


    Organizational Affiliation

    Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC, H3A 2B4, Canada.,Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada. martin.schmeing@mcgill.ca.,Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.,Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC, H3A 2B4, Canada. gregory.marczynski@mcgill.ca.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth 15 Road, Ottawa, ON, K1H 8L1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UPF0335 protein CC_3319
A
113Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 0 
Find proteins for Q9A385 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9A385
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.851 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • Space Group: I 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 116.481α = 90.00
b = 116.481β = 90.00
c = 116.481γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN-148472
Canadian Institutes of Health Research (CIHR)CanadaMOP-125998

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release