8DMT | pdb_00008dmt

Crystal structure of macrodomain CG2909 from Drosophila melanogaster in complex with ADP-ribose

  • Classification: HYDROLASE
  • Organism(s): Drosophila melanogaster
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-07-08 Released: 2023-08-02 
  • 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: 2.28 Å
  • R-Value Free: 
    0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: in silico
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This is version 1.3 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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RE54994p
A, B, C, D
492Drosophila melanogasterMutation(s): 0 
Gene Names: Dmel\CG2909CG2909Dmel_CG2909
EC: 3.2.2.19
UniProt
Find proteins for Q9W2W5 (Drosophila melanogaster)
Explore Q9W2W5 
Go to UniProtKB:  Q9W2W5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9W2W5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.949α = 90
b = 90.006β = 95.89
c = 212.267γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2023-08-02
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection
  • Version 1.2: 2024-07-24
    Changes: Database references
  • Version 1.3: 2026-03-04
    Changes: Derived calculations, Refinement description, Structure summary