TraI trans-esterase domain from pKM101 (apo)

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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This is version 1.2 of the entry. See complete history


Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing.

Breidenstein, A.Ter Beek, J.Berntsson, R.P.

(2023) Life Sci Alliance 6

  • DOI: https://doi.org/10.26508/lsa.202201775
  • Primary Citation of Related Structures:  
    8A1B, 8A1C

  • PubMed Abstract: 

    Type 4 secretion systems are large and versatile protein machineries that facilitate the spread of antibiotic resistance and other virulence factors via horizontal gene transfer. Conjugative type 4 secretion systems depend on relaxases to process the DNA in preparation for transport. TraI from the well-studied conjugative plasmid pKM101 is one such relaxase. Here, we report the crystal structure of the trans-esterase domain of TraI in complex with its substrate oriT DNA, highlighting the conserved DNA-binding mechanism of conjugative relaxases. In addition, we present an apo structure of the trans-esterase domain of TraI that includes most of the flexible thumb region. This allows us for the first time to visualize the large conformational change of the thumb subdomain upon DNA binding. We also characterize the DNA binding, nicking, and religation activity of the trans-esterase domain, helicase domain, and full-length TraI. Unlike previous indications in the literature, our results reveal that the TraI trans-esterase domain from pKM101 behaves in a conserved manner with its homologs from the R388 and F plasmids.

  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TraI306Escherichia coliMutation(s): 0 
Gene Names: traI
Find proteins for D9Z5Q2 (Escherichia coli)
Explore D9Z5Q2 
Go to UniProtKB:  D9Z5Q2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9Z5Q2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.166α = 90
b = 80.628β = 90
c = 90.575γ = 90
Software Package:
Software NamePurpose
AutoProcessdata processing
Cootmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
Swedish Research CouncilSweden2016-03599

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description