6DGB

Crystal structure of the C-terminal catalytic domain of IS1535 TnpA, an IS607-like serine recombinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transposition.

Chen, W.Mandali, S.Hancock, S.P.Kumar, P.Collazo, M.Cascio, D.Johnson, R.C.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.39611
  • Primary Citation of Related Structures:  
    6DGB, 6DGC

  • PubMed Abstract: 

    IS 607 -family transposons are unusual because they do not have terminal inverted repeats or generate target site duplications. They encode two protein-coding genes, but only tnpA is required for transposition. Our X-ray structures confirm that TnpA is a member of the serine recombinase (SR) family, but the chemically-inactive quaternary structure of the dimer, along with the N-terminal location of the DNA binding domain, are different from other SRs. TnpA dimers from IS 1535 cooperatively associate with multiple subterminal repeats, which together with additional nonspecific binding, form a nucleoprotein filament on one transposon end that efficiently captures a second unbound end to generate the paired-end complex (PEC). Formation of the PEC does not require a change in the dimeric structure of the catalytic domain, but remodeling of the C-terminal α-helical region is involved. We posit that the PEC recruits a chemically-active conformer of TnpA to the transposon end to initiate DNA chemistry.


  • Organizational Affiliation

    Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IS607 family transposase IS1535
A, B
143Mycobacterium tuberculosisMutation(s): 0 
Gene Names: IS1535 TnpA
UniProt
Find proteins for I6WZS4 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6WZS4 
Go to UniProtKB:  I6WZS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6WZS4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.56α = 90
b = 54.18β = 90
c = 104.28γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM038509

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references