1P4D

F factor TraI Relaxase Domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 

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

  • Also Cited By: 2A0I

  • 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 th ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TraI protein
A, B, C
330Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: traI
Find proteins for P14565 (Escherichia coli (strain K12))
Go to UniProtKB:  P14565
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.219α = 90.00
b = 128.219β = 90.00
c = 121.184γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SnBphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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