6DGB | pdb_00006dgb

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 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6DGB

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 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.

Macromolecule Content 

  • Total Structure Weight: 31.49 kDa 
  • Atom Count: 2,026 
  • Modeled Residue Count: 265 
  • Deposited Residue Count: 286 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
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