1P4D

F factor TraI Relaxase Domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structural insights into single-stranded DNA binding and cleavage by F factor TraI.

Datta, S., Larkin, C., Schildbach, J.F.

(2003) Structure 11: 1369-1379

  • DOI: 10.1016/j.str.2003.10.001
  • Primary Citation of Related Structures:  
    1P4D

  • PubMed Abstract: 

    • Conjugative plasmid transfer between bacteria disseminates antibiotic resistance and diversifies prokaryotic genomes. Relaxases, proteins essential for conjugation, cleave one plasmid strand sequence specifically prior to transfer. Cleavage occurs through a Mg(2+)-dependent transesterification involving a tyrosyl hydroxyl and a DNA phosphate ...

    Conjugative plasmid transfer between bacteria disseminates antibiotic resistance and diversifies prokaryotic genomes. Relaxases, proteins essential for conjugation, cleave one plasmid strand sequence specifically prior to transfer. Cleavage occurs through a Mg(2+)-dependent transesterification involving a tyrosyl hydroxyl and a DNA phosphate. The structure of the F plasmid TraI relaxase domain, described here, is a five-strand beta sheet flanked by alpha helices. The protein resembles replication initiator protein AAV-5 Rep but is circularly permuted, yielding a different topology. The beta sheet forms a binding cleft lined with neutral, nonaromatic residues, unlike most single-stranded DNA binding proteins which use aromatic and charged residues. The cleft contains depressions, suggesting base recognition occurs in a knob-into-hole fashion. Unlike most nucleases, three histidines but no acidic residues coordinate a Mg(2+) located near the catalytic tyrosine. The full positive charge on the Mg(2+) and the architecture of the active site suggest multiple roles for Mg(2+) in DNA cleavage.

    Related Citations: 
    • Subdomain organization and catalytic residues of the F factor TraI relaxase domain
      Street, L.M., Harley, M.J., Stern, J.C., Larkin, C., Williams, S.L., Miller, D.L., Dohm, J.A., Rodgers, M.E., Schildbach, J.F.
      (2003) Biochim Biophys Acta 1646: 86
    Organizational Affiliation: 

    Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TraI proteinA, B, C330Escherichia coliMutation(s): 0 
Gene Names: traI
EC: 3.6.1 (PDB Primary Data), 5.6.2.1 (UniProt), 3.6.4.12 (UniProt)
UniProt
Find proteins for P14565 (Escherichia coli (strain K12))
Explore P14565 
Go to UniProtKB:  P14565
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14565
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.219α = 90
b = 128.219β = 90
c = 121.184γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-10-11
    Changes: Refinement description