Crystal structure of Antirestriction ArdC protein from R388 plasmid. Metal-free structure.

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

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ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range.

Gonzalez-Montes, L.Del Campo, I.Garcillan-Barcia, M.P.de la Cruz, F.Moncalian, G.

(2020) PLoS Genet 16: e1008750-e1008750

  • DOI: https://doi.org/10.1371/journal.pgen.1008750
  • Primary Citation of Related Structures:  
    6I89, 6SNA

  • PubMed Abstract: 

    Plasmids, when transferred by conjugation in natural environments, must overpass restriction-modification systems of the recipient cell. We demonstrate that protein ArdC, encoded by broad host range plasmid R388, was required for conjugation from Escherichia coli to Pseudomonas putida. Expression of ardC was required in the recipient cells, but not in the donor cells. Besides, ardC was not required for conjugation if the hsdRMS system was deleted in P. putida recipient cells. ardC was also required if the hsdRMS system was present in E. coli recipient cells. Thus, ArdC has antirestriction activity against the HsdRMS system and consequently broadens R388 plasmid host range. The crystal structure of ArdC was solved both in the absence and presence of Mn2+. ArdC is composed of a non-specific ssDNA binding N-terminal domain and a C-terminal metalloprotease domain, although the metalloprotease activity was not needed for the antirestriction function. We also observed by RNA-seq that ArdC-dependent conjugation triggered an SOS response in the P. putida recipient cells. Our findings give new insights, and open new questions, into the antirestriction strategies developed by plasmids to counteract bacterial restriction strategies and settle into new hosts.

  • Organizational Affiliation

    Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Cantabria, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ArdC protein297Escherichia coliMutation(s): 0 
Gene Names: ardC
Find proteins for Q6I6B2 (Escherichia coli)
Explore Q6I6B2 
Go to UniProtKB:  Q6I6B2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6I6B2
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.798α = 90
b = 136.798β = 90
c = 51.701γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-55534-C2-2-P
Spanish Ministry of Science, Innovation, and UniversitiesSpainFPU014/0601

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references