9EMK | pdb_00009emk

DupA from legionella covalently bound to ubiquitin-based probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.239 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Covalent Probes To Capture Legionella pneumophila Dup Effector Enzymes.

Kloet, M.S.Mukhopadhyay, R.Mukherjee, R.Misra, M.Jeong, M.Talavera Ormeno, C.M.P.Moutsiopoulou, A.Tjokrodirijo, R.T.N.van Veelen, P.A.Shin, D.Dikic, I.Sapmaz, A.Kim, R.Q.van der Heden van Noort, G.J.

(2024) J Am Chem Soc 146: 26957-26964

  • DOI: https://doi.org/10.1021/jacs.4c08168
  • Primary Citation of Related Structures:  
    9EMK

  • PubMed Abstract: 

    Upon infection of host cells, Legionella pneumophila releases a multitude of effector enzymes into the cell's cytoplasm that hijack a plethora of cellular activities, including the host ubiquitination pathways. Effectors belonging to the SidE-family are involved in noncanonical serine phosphoribosyl ubiquitination of host substrate proteins contributing to the formation of a Legionella-containing vacuole that is crucial in the onset of Legionnaires' disease. This dynamic process is reversed by effectors called Dups that hydrolyze the phosphodiester in the phosphoribosyl ubiquitinated protein. We installed reactive warheads on chemically prepared ribosylated ubiquitin to generate a set of probes targeting these Legionella enzymes. In vitro tests on recombinant DupA revealed that a vinyl sulfonate warhead was most efficient in covalent complex formation. Mutagenesis and X-ray crystallography approaches were used to identify the site of covalent cross-linking to be an allosteric cysteine residue. The subsequent application of this probe highlights the potential to selectively enrich the Dup enzymes from Legionella-infected cell lysates.


  • Organizational Affiliation
    • Department of Cell and Chemical Biology, Leiden University Medical Centre, 2333 ZC, Leiden, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Septation initiation protein
A, C, E
347Legionella pneumophila subsp. pneumophilaMutation(s): 0 
Gene Names: D1H98_09620
UniProt
Find proteins for A0A3A6VNK6 (Legionella pneumophila subsp. pneumophila)
Explore A0A3A6VNK6 
Go to UniProtKB:  A0A3A6VNK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3A6VNK6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-B
B, D, F
76Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
B, D, F
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.239 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.808α = 90
b = 86.808β = 90
c = 146.539γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)NetherlandsVI.Vidi.192.011
European Research Council (ERC)European Union101087582
H2020 Marie Curie Actions of the European CommissionEuropean UnionH2020-MSCA-ITN-2018

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release