1U78

Structure of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA

Watkins, S.van Pouderoyen, G.Sixma, T.K.

(2004) Nucleic Acids Res. 32: 4306-4312

  • DOI: 10.1093/nar/gkh770

  • PubMed Abstract: 
  • The bipartite DNA-binding domain of Tc3 transposase, Tc3A, was crystallized in complex with its transposon recognition sequence. In the structure the two DNA-binding domains form structurally related helix-turn-helix (HTH) motifs. They both bind to t ...

    The bipartite DNA-binding domain of Tc3 transposase, Tc3A, was crystallized in complex with its transposon recognition sequence. In the structure the two DNA-binding domains form structurally related helix-turn-helix (HTH) motifs. They both bind to the major groove on a single DNA oligomer, separated by a linker that interacts closely with the minor groove. The structure resembles that of the transcription factor Pax6 DNA-binding domain, but the relative orientation of the HTH-domain is different. The DNA conformation is distorted, characterized by local narrowing of the minor groove and bends at both ends. The protein-DNA recognition takes place through base and backbone contacts, as well as shape-recognition of the distortions in the DNA. Charged interactions are primarily found in the N-terminal domain and the linker indicating that these may form the initial contact area. Two independent dimer interfaces could be relevant for bringing together transposon ends and for binding to a direct repeat site in the transposon end. In contrast to the Tn5 synaptic complex, the two Tc3A DNA-binding domains bind to a single Tc3 transposon end.


    Organizational Affiliation

    Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
transposable element tc3 transposase
A
141Caenorhabditis elegansGene Names: tc3a
Find proteins for P34257 (Caenorhabditis elegans)
Go to UniProtKB:  P34257
Entity ID: 1
MoleculeChainsLengthOrganism
26-MERB26N/A
Entity ID: 2
MoleculeChainsLengthOrganism
26-MERC26N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.233 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.681α = 90.00
b = 93.681β = 90.00
c = 255.558γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance