1MM8

Crystal structure of Tn5 Transposase complexed with ME DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evidence for "unseen" Transposase--DNA contacts

Steiniger-White, M.Bhasin, A.Lovell, S.Rayment, I.Reznikoff, W.S.

(2002) J Mol Biol 322: 971-982

  • DOI: 10.1016/s0022-2836(02)00877-x
  • Primary Citation of Related Structures:  
    1MM8

  • PubMed Abstract: 
  • In this study, evidence of novel, important interactions between a hyperactive Tn5 transposon recognition end sequence and hyperactive Tn5 transposase (Tnp) are presented. A hyperactive Tn5 end sequence, the mosaic end (ME), was isolated previously. The ME and a wild-type end sequence, the outside end (OE), differ at only three positions, yet transposition on the ME is tenfold higher than on the OE in vivo ...

    In this study, evidence of novel, important interactions between a hyperactive Tn5 transposon recognition end sequence and hyperactive Tn5 transposase (Tnp) are presented. A hyperactive Tn5 end sequence, the mosaic end (ME), was isolated previously. The ME and a wild-type end sequence, the outside end (OE), differ at only three positions, yet transposition on the ME is tenfold higher than on the OE in vivo. Also, transposition on the ME is much more efficient than transposition on the OE in vitro. Here, we show that the decreased activity observed for the OE is caused by a defect in paired ends complex (PEC) formation resulting from the orientation of the A-T base-pair at position 4 of this end. Efficient PEC formation requires an interaction between the C5-methyl group (C5-Me) on the non-transferred strand thymine base at position 4 (T4) and Tnp. PEC formation on nicked substrates is much less affected by the orientation of the A-T base-pair at position 4, indicating that the C5-Me group is important only for steps preceding nicking. A recently determined co-crystal structure of Tn5 Tnp with the ME is discussed and a model explaining possible roles for the base-pair at position 4 is explored.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tn5 TransposaseC [auth A]481Escherichia coliMutation(s): 4 
Gene Names: Tn5 TransposasestnpAtnp
EC: 3.1
UniProt
Find proteins for Q46731 (Escherichia coli)
Explore Q46731 
Go to UniProtKB:  Q46731
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    ME DNA transferred strandA [auth B]20N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      ME DNA non-transferred strandB [auth C]20N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MN
      Query on MN

      Download Ideal Coordinates CCD File 
      D [auth A], E [auth A]MANGANESE (II) ION
      Mn
      WAEMQWOKJMHJLA-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.271 
      • R-Value Work: 0.217 
      • Space Group: P 65 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 112.5α = 90
      b = 112.5β = 90
      c = 233.5γ = 120
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      SCALEPACKdata scaling
      EPMRphasing
      CNSrefinement
      HKL-2000data reduction

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2002-12-13
        Type: Initial release
      • Version 1.1: 2008-04-28
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2021-10-27
        Changes: Database references, Derived calculations