8SSI

Structure of Burkholderia pseudomallei deubiquitinase TssM in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bacterial esterases reverse lipopolysaccharide ubiquitylation to block host immunity.

Szczesna, M.Huang, Y.Lacoursiere, R.E.Bonini, F.Pol, V.Koc, F.Ward, B.Geurink, P.P.Pruneda, J.N.Thurston, T.L.M.

(2024) Cell Host Microbe 32: 913-924.e7

  • DOI: https://doi.org/10.1016/j.chom.2024.04.012
  • Primary Citation of Related Structures:  
    8SSI

  • PubMed Abstract: 

    Aspects of how Burkholderia escape the host's intrinsic immune response to replicate in the cell cytosol remain enigmatic. Here, we show that Burkholderia has evolved two mechanisms to block the activity of Ring finger protein 213 (RNF213)-mediated non-canonical ubiquitylation of bacterial lipopolysaccharide (LPS), thereby preventing the initiation of antibacterial autophagy. First, Burkholderia's polysaccharide capsule blocks RNF213 association with bacteria and second, the Burkholderia deubiquitylase (DUB), TssM, directly reverses the activity of RNF213 through a previously unrecognized esterase activity. Structural analysis provides insight into the molecular basis of TssM esterase activity, allowing it to be uncoupled from its isopeptidase function. Furthermore, a putative TssM homolog also displays esterase activity and removes ubiquitin from LPS, establishing this as a virulence mechanism. Of note, we also find that additional immune-evasion mechanisms exist, revealing that overcoming this arm of the host's immune response is critical to the pathogen.


  • Organizational Affiliation

    Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deubiquitinase TssM
A, C
288Burkholderia pseudomalleiMutation(s): 0 
Gene Names: BPSS1512
UniProt
Find proteins for Q63K53 (Burkholderia pseudomallei (strain K96243))
Explore Q63K53 
Go to UniProtKB:  Q63K53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63K53
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin
B, D
75Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.517α = 90
b = 104.517β = 90
c = 193.801γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM142486
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R011834/1
Wellcome TrustUnited Kingdom209411/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references, Derived calculations, Structure summary