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 
  • R-Value Observed: 0.235 

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This is version 1.3 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: https://doi.org/10.1093/nar/gkh770
  • Primary Citation of Related Structures:  
    1U78

  • 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 the major groove on a single DNA oligomer, separated by a linker that interacts closely with the minor groove ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
transposable element tc3 transposaseC [auth A]141Caenorhabditis elegansMutation(s): 1 
Gene Names: Tc3, tc3a, B0303.5
UniProt
Find proteins for P34257 (Caenorhabditis elegans)
Explore P34257 
Go to UniProtKB:  P34257
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34257
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
26-MERA [auth B]26N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
26-MERB [auth C]26N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.681α = 90
b = 93.681β = 90
c = 255.558γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Data collection, Database references