6XG8

ISCth4 transposase, pre-cleaved complex, PCC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report



Literature

Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition.

Kosek, D.Hickman, A.B.Ghirlando, R.He, S.Dyda, F.

(2020) EMBO J : e105666-e105666

  • DOI: 10.15252/embj.2020105666
  • Primary Citation of Related Structures:  
    6XG8, 6XGX, 6XGW

  • PubMed Abstract: 
  • Copy-out/paste-in transposition is a major bacterial DNA mobility pathway. It contributes significantly to the emergence of antibiotic resistance, often by upregulating expression of downstream genes upon integration. Unlike other transposition pathw ...

    Copy-out/paste-in transposition is a major bacterial DNA mobility pathway. It contributes significantly to the emergence of antibiotic resistance, often by upregulating expression of downstream genes upon integration. Unlike other transposition pathways, it requires both asymmetric and symmetric strand transfer steps. Here, we report the first structural study of a copy-out/paste-in transposase and demonstrate its ability to catalyze all pathway steps in vitro. X-ray structures of ISCth4 transposase, a member of the IS256 family of insertion sequences, bound to DNA substrates corresponding to three sequential steps in the reaction reveal an unusual asymmetric dimeric transpososome. During transposition, an array of N-terminal domains binds a single transposon end while the catalytic domain moves to accommodate the varying substrates. These conformational changes control the path of DNA flanking the transposon end and the generation of DNA-binding sites. Our results explain the asymmetric outcome of the initial strand transfer and show how DNA binding is modulated by the asymmetric transposase to allow the capture of a second transposon end and to integrate a circular intermediate.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mutator family transposaseAB410Hungateiclostridium thermocellum ATCC 27405Mutation(s): 0 
Gene Names: Cthe_0148Cthe_0356Cthe_0371Cthe_1193Cthe_1874Cthe_3051
Find proteins for A3DBR0 (Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DBR0 
Go to UniProtKB:  A3DBR0
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (26-MER)D26Hungateiclostridium thermocellum ATCC 27405
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (26-MER)E26Hungateiclostridium thermocellum ATCC 27405
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.68α = 90
b = 109.5β = 90
c = 157.7γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2020-06-17 
  • Released Date: 2020-10-14 
  • Deposition Author(s): Kosek, D., Dyda, F.

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release