8DMP | pdb_00008dmp

Crystal structure of Legionella pneumophila macrodomain effector MavL

  • Classification: ANTITOXIN
  • Organism(s): Legionella pneumophila
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-07-08 Released: 2023-07-12 
  • Deposition Author(s): Zhang, Z., Das, C.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8DMP

This is version 1.2 of the entry. See complete history

Literature

Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain.

Zhang, Z.Fu, J.Rack, J.G.M.Li, C.Voorneveld, J.Filippov, D.V.Ahel, I.Luo, Z.Q.Das, C.

(2024) Nat Commun 15: 2452-2452

  • DOI: https://doi.org/10.1038/s41467-024-46649-2
  • Primary Citation Related Structures: 
    8DMP, 8DMQ, 8DMR, 8DMS, 8DMT, 8DMU

  • PubMed Abstract: 

    ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster. Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.


  • Organizational Affiliation
    • Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.

Macromolecule Content 

  • Total Structure Weight: 353.45 kDa 
  • Atom Count: 24,110 
  • Modeled Residue Count: 2,963 
  • Deposited Residue Count: 3,192 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MavL
A, B, C, D, E
A, B, C, D, E, F, G, H
399Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZSJ1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZSJ1 
Go to UniProtKB:  Q5ZSJ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZSJ1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.232α = 90
b = 157.244β = 96.2
c = 117.621γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01GM126296
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesT32AI148103

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-07-24
    Changes: Database references