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:  
    2VHG, 2VIC, 2VIH, 2VJU, 2VJV

  • 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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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSPOSASE ORFAA, B159Helicobacter pyloriMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q933Z0 (Helicobacter pylori)
Explore Q933Z0 
Go to UniProtKB:  Q933Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ933Z0
Protein Feature View
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  • Reference Sequence
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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, D 26Helicobacter pylori
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*DT*DA*DT*DT*DA*DCP)-3'E, F 6Helicobacter pylori
Protein Feature View
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  • Reference Sequence
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

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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