2VJV

Crystal structure of the IS608 transposase in complex with left end 26-mer DNA hairpin and a 6-mer DNA representing the left end cleavage site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection.

Barabas, O., Ronning, D.R., Guynet, C., Hickman, A.B., Ton-Hoang, B., Chandler, M., Dyda, F.

(2008) Cell 132: 208

  • DOI: 10.1016/j.cell.2007.12.029
  • Primary Citation of Related Structures:  
    2VIC, 2VHG, 2VIH, 2VJV, 2VJU

  • PubMed Abstract: 

    • The smallest known DNA transposases are those from the IS200/IS605 family. Here we show how the interplay of protein and DNA activates TnpA, the Helicobacter pylori IS608 transposase, for catalysis. First, transposon end binding causes a conformational change that aligns catalytically important protein residues within the active site ...

    The smallest known DNA transposases are those from the IS200/IS605 family. Here we show how the interplay of protein and DNA activates TnpA, the Helicobacter pylori IS608 transposase, for catalysis. First, transposon end binding causes a conformational change that aligns catalytically important protein residues within the active site. Subsequent precise cleavage at the left and right ends, the steps that liberate the transposon from its donor site, does not involve a site-specific DNA-binding domain. Rather, cleavage site recognition occurs by complementary base pairing with a TnpA-bound subterminal transposon DNA segment. Thus, the enzyme active site is constructed from elements of both protein and DNA, reminiscent of the interdependence of protein and RNA in the ribosome. Our structural results explain why the transposon ends are asymmetric and how the transposon selects a target site for integration, and they allow us to propose a molecular model for the entire transposition reaction.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSPOSASE ORFAA, B159Helicobacter pyloriMutation(s): 0 
Gene Names: 
Find proteins for Q933Z0 (Helicobacter pylori)
Explore Q933Z0 
Go to UniProtKB:  Q933Z0
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT *DT*DT*DA*DG*DC*DT*DA*DT*DG*DG*DG*DGP)-3'C, D26Helicobacter pylori
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-D(*DT*DA*DT*DT*DA*DCP)-3'E, F6Helicobacter pylori
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG
    Download Ideal Coordinates CCD File 
    		 G [auth C], H [auth D], I [auth E]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.90 Å
    • R-Value Free: 0.227 
    • R-Value Work: 0.194 
    • R-Value Observed: 0.194 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 66.292α = 90
    b = 72.407β = 90
    c = 110.174γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    AMoREphasing

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2008-02-19
      Type: Initial release
    • Version 1.1: 2011-05-08
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance