6DWW

Hermes transposase deletion dimer complex with (A/T) DNA and Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase.

Hickman, A.B.Voth, A.R.Ewis, H.Li, X.Craig, N.L.Dyda, F.

(2018) Nucleic Acids Res 46: 10286-10301

  • DOI: 10.1093/nar/gky838
  • Primary Citation of Related Structures:  
    6DWZ, 6DWY, 6DWW, 6DX0

  • PubMed Abstract: 
  • Some DNA transposons relocate from one genomic location to another using a mechanism that involves generating double-strand breaks at their transposon ends by forming hairpins on flanking DNA. The same double-strand break mode is employed by the V(D)J recombinase at signal-end/coding-end junctions during the generation of antibody diversity ...

    Some DNA transposons relocate from one genomic location to another using a mechanism that involves generating double-strand breaks at their transposon ends by forming hairpins on flanking DNA. The same double-strand break mode is employed by the V(D)J recombinase at signal-end/coding-end junctions during the generation of antibody diversity. How flanking hairpins are formed during DNA transposition has remained elusive. Here, we describe several co-crystal structures of the Hermes transposase bound to DNA that mimics the reaction step immediately prior to hairpin formation. Our results reveal a large DNA conformational change between the initial cleavage step and subsequent hairpin formation that changes which strand is acted upon by a single active site. We observed that two factors affect the conformational change: the complement of divalent metal ions bound by the catalytically essential DDE residues, and the identity of the -2 flanking base pair. Our data also provides a mechanistic link between the efficiency of hairpin formation (an A:T basepair is favored at the -2 position) and Hermes' strong target site preference. Furthermore, we have established that the histidine residue within a conserved C/DxxH motif present in many transposase families interacts directly with the scissile phosphate, suggesting a crucial role in catalysis.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hermes transposaseA517Musca domesticaMutation(s): 1 
UniProt
Find proteins for Q25438 (Musca domestica)
Explore Q25438 
Go to UniProtKB:  Q25438
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*AP*GP*AP*AP*CP*AP*AP*CP*AP*AP*CP*AP*AP*G)-3')B16Musca domestica
    Protein Feature View
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (25-MER)C25Musca domestica
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*GP*TP*GP*AP*A)-3')D7Musca domestica
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MN
      Query on MN

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.85 Å
      • R-Value Free: 0.264 
      • R-Value Work: 0.199 
      • R-Value Observed: 0.202 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 122.48α = 90
      b = 136.46β = 90
      c = 104.61γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      XDSdata scaling
      AMoREphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2018-09-19
        Type: Initial release
      • Version 1.1: 2019-01-23
        Changes: Data collection, Database references