5VFX

Structure of an accessory protein of the pCW3 relaxosome in complex with the origin of transfer (oriT) DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3.

Traore, D.A.K.Wisniewski, J.A.Flanigan, S.F.Conroy, P.J.Panjikar, S.Mok, Y.F.Lao, C.Griffin, M.D.W.Adams, V.Rood, J.I.Whisstock, J.C.

(2018) Nat Commun 9: 3732-3732

  • DOI: 10.1038/s41467-018-06096-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Conjugation is fundamental for the acquisition of new genetic traits and the development of antibiotic resistance in pathogenic organisms. Here, we show that a hypothetical Clostridium perfringens protein, TcpK, which is encoded by the tetracycline r ...

    Conjugation is fundamental for the acquisition of new genetic traits and the development of antibiotic resistance in pathogenic organisms. Here, we show that a hypothetical Clostridium perfringens protein, TcpK, which is encoded by the tetracycline resistance plasmid pCW3, is essential for efficient conjugative DNA transfer. Our studies reveal that TcpK is a member of the winged helix-turn-helix (wHTH) transcription factor superfamily and that it forms a dimer in solution. Furthermore, TcpK specifically binds to a nine-nucleotide sequence that is present as tandem repeats within the pCW3 origin of transfer (oriT). The X-ray crystal structure of the TcpK-TcpK box complex reveals a binding mode centered on and around the β-wing, which is different from what has been previously shown for other wHTH proteins. Structure-guided mutagenesis experiments validate the specific interaction between TcpK and the DNA molecule. Additional studies highlight that the TcpK dimer is important for specific DNA binding.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TcpK
A, B, C, D, E, F, G, H
107Clostridium perfringensMutation(s): 0 
Find proteins for Q1PLI2 (Clostridium perfringens)
Go to UniProtKB:  Q1PLI2
Entity ID: 2
MoleculeChainsLengthOrganism
oriTI,K,N,O23Clostridium perfringens
Entity ID: 3
MoleculeChainsLengthOrganism
oriTJ,L,M,P23Clostridium perfringens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.503α = 90.00
b = 109.894β = 93.02
c = 122.780γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
BUSTERrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Database references