6HV6

Crystal structure of PatoxP, a cysteine protease-like domain of Photorhabdus asymbiotica toxin PaTox


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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This is version 1.2 of the entry. See complete history


Literature

A cysteine protease-like domain enhances the cytotoxic effects of thePhotorhabdus asymbioticatoxin PaTox.

Bogdanovic, X.Schneider, S.Levanova, N.Wirth, C.Trillhaase, C.Steinemann, M.Hunte, C.Aktories, K.Jank, T.

(2019) J Biol Chem 294: 1035-1044

  • DOI: https://doi.org/10.1074/jbc.RA118.005043
  • Primary Citation of Related Structures:  
    6HV6

  • PubMed Abstract: 

    The nematode mutualistic bacterium Photorhabdus asymbiotica produces a large virulence-associated multifunctional protein toxin named PaTox. A glycosyltransferase domain and a deamidase domain of this large toxin function as effectors that specifically target host Rho GTPases and heterotrimeric G proteins, respectively. Modification of these intracellular regulators results in toxicity toward insects and mammalian cells. In this study, we identified a cysteine protease-like domain spanning PaTox residues 1844-2114 (PaTox P ), upstream of these two effector domains and characterized by three conserved amino acid residues (Cys-1865, His-1955, and Asp-1975). We determined the crystal structure of the PaTox P C1865A variant by native single-wavelength anomalous diffraction of sulfur atoms (sulfur-SAD). At 2.0 Å resolution, this structure revealed a catalytic site typical for papain-like cysteine proteases, comprising a catalytic triad, oxyanion hole, and typical secondary structural elements. The PaTox P structure had highest similarity to that of the AvrPphB protease from Pseudomonas syringae classified as a C58-protease. Furthermore, we observed that PaTox P shares structural homology also with non-C58-cysteine proteases, deubiquitinases, and deamidases. Upon delivery into insect larvae, PaTox P alone without full-length PaTox had no toxic effects. Yet, PaTox P expression in mammalian cells was toxic and enhanced the apoptotic phenotype induced by PaTox in HeLa cells. We propose that PaTox P is a C58-like cysteine protease module that is essential for full PaTox activity.


  • Organizational Affiliation

    From the Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin PAU_02230463Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949Mutation(s): 1 
Gene Names: PAU_02230
EC: 2.4.1 (PDB Primary Data), 3.5.1.44 (PDB Primary Data)
UniProt
Find proteins for C7BKP9 (Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77))
Explore C7BKP9 
Go to UniProtKB:  C7BKP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7BKP9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.403α = 90
b = 76.029β = 90
c = 76.324γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCRC 746
GermanyEXC 294 BIOSS

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.2: 2022-07-13
    Changes: Advisory, Database references, Structure summary