1TC3

TRANSPOSASE TC3A1-65 FROM CAENORHABDITIS ELEGANS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.318 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA.

van Pouderoyen, G.Ketting, R.F.Perrakis, A.Plasterk, R.H.Sixma, T.K.

(1997) EMBO J 16: 6044-6054

  • DOI: 10.1093/emboj/16.19.6044
  • Primary Citation of Related Structures:  
    1TC3

  • PubMed Abstract: 
  • The crystal structure of the complex between the N-terminal DNA-binding domain of Tc3 transposase and an oligomer of transposon DNA has been determined. The specific DNA-binding domain contains three alpha-helices, of which two form a helix-turn-helix (HTH) motif ...

    The crystal structure of the complex between the N-terminal DNA-binding domain of Tc3 transposase and an oligomer of transposon DNA has been determined. The specific DNA-binding domain contains three alpha-helices, of which two form a helix-turn-helix (HTH) motif. The recognition of transposon DNA by the transposase is mediated through base-specific contacts and complementarity between protein and sequence-dependent deformations of the DNA. The HTH motif makes four base-specific contacts with the major groove, and the N-terminus makes three base-specific contacts with the minor groove. The DNA oligomer adopts a non-linear B-DNA conformation, made possible by a stretch of seven G:C base pairs at one end and a TATA sequence towards the other end. Extensive contacts (seven salt bridges and 16 hydrogen bonds) of the protein with the DNA backbone allow the protein to probe and recognize the sequence-dependent DNA deformation. The DNA-binding domain forms a dimer in the crystals. Each monomer binds a separate transposon end, implying that the dimer plays a role in synapsis, necessary for the simultaneous cleavage of both transposon termini.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (TC3 TRANSPOSASE)C51Caenorhabditis elegansMutation(s): 0 
Gene Names: tc3aB0303.5
Find proteins for P34257 (Caenorhabditis elegans)
Explore P34257 
Go to UniProtKB:  P34257
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*GP*TP*CP*CP*TP*AP*TP*AP*GP*A P*AP*CP*TP*T)-3')A21N/A
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*TP*TP*CP*TP*AP*TP*AP*GP*GP*AP*CP*CP*CP*CP*C P*CP*CP*T)-3')B20N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.45 Å
    • R-Value Free: 0.318 
    • R-Value Observed: 0.234 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 37.18α = 90
    b = 202.79β = 90
    c = 62.14γ = 90
    Software Package:
    Software NamePurpose
    PHASESphasing
    TNTrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1997-11-21
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance