4PCB

Conjugative Relaxase TrwC in complex with mutant OriT Dna


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A high security double lock and key mechanism in HUH relaxases controls oriT-processing for plasmid conjugation.

Carballeira, J.D.Gonzalez-Perez, B.Moncalian, G.la Cruz, F.d.

(2014) Nucleic Acids Res. 42: 10632-10643

  • DOI: 10.1093/nar/gku741

  • PubMed Abstract: 
  • Relaxases act as DNA selection sieves in conjugative plasmid transfer. Most plasmid relaxases belong to the HUH endonuclease family. TrwC, the relaxase of plasmid R388, is the prototype of the HUH relaxase family, which also includes TraI of plasmid ...

    Relaxases act as DNA selection sieves in conjugative plasmid transfer. Most plasmid relaxases belong to the HUH endonuclease family. TrwC, the relaxase of plasmid R388, is the prototype of the HUH relaxase family, which also includes TraI of plasmid F. In this article we demonstrate that TrwC processes its target nic-site by means of a highly secure double lock and key mechanism. It is controlled both by TrwC-DNA intermolecular interactions and by intramolecular DNA interactions between several nic nucleotides. The sequence specificity map of the interaction between TrwC and DNA was determined by systematic mutagenesis using degenerate oligonucleotide libraries. The specificity map reveals the minimal nic sequence requirements for R388-based conjugation. Some nic-site sequence variants were still able to form the U-turn shape at the nic-site necessary for TrwC processing, as observed by X-ray crystallography. Moreover, purified TrwC relaxase effectively cleaved ssDNA as well as dsDNA substrates containing these mutant sequences. Since TrwC is able to catalyze DNA integration in a nic-site-containing DNA molecule, characterization of nic-site functionally active sequence variants should improve the search quality of potential target sequences for relaxase-mediated integration in any target genome.


    Organizational Affiliation

    Departamento de BiologĂ­a Molecular e Instituto de Biomedicina y BiotecnologĂ­a de Cantabria, IBBTEC, Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011 Santander, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TrwC
A, C
293Escherichia coliMutation(s): 0 
Gene Names: trwC
Find proteins for Q47673 (Escherichia coli)
Go to UniProtKB:  Q47673
Entity ID: 2
MoleculeChainsLengthOrganism
DNA 5'-D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3')B,D24Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.255 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 148.690α = 90.00
b = 148.690β = 90.00
c = 77.810γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
iMOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of EconomySpainBIO2008-00140 and BIO2010- 14809

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references
  • Version 1.2: 2014-12-24
    Type: Database references