8DMQ | pdb_00008dmq

Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.209 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8DMQ

This is version 2.1 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: 107.01 kDa 
  • Atom Count: 7,348 
  • Modeled Residue Count: 888 
  • Deposited Residue Count: 948 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MavL
A, B
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin
C, D
75Homo sapiensMutation(s): 0 
Gene Names: UBB
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
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
N [auth D]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
FLC

Query on FLC



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth B],
M [auth C]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
GVE

Query on GVE



Download:Ideal Coordinates CCD File
J [auth C],
O [auth D]
METHYL 4-AMINOBUTANOATE
C5 H11 N O2
KVQGGLZHHFGHPU-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth B],
K [auth C],
L [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.209 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.719α = 90
b = 108.719β = 90
c = 209.143γ = 120
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 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-07-24
    Changes: Database references