6B7O

Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector.

Akturk, A.Wasilko, D.J.Wu, X.Liu, Y.Zhang, Y.Qiu, J.Luo, Z.Q.Reiter, K.H.Brzovic, P.S.Klevit, R.E.Mao, Y.

(2018) Nature 557: 729-733

  • DOI: 10.1038/s41586-018-0147-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitination is a post-translational modification that regulates many cellular processes in eukaryotes <sup>1-4 </sup>. The conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target p ...

    Ubiquitination is a post-translational modification that regulates many cellular processes in eukaryotes 1-4 . The conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein, usually on a lysine side chain 1,5 . Recent studies of the Legionella pneumophila SidE family of effector proteins revealed a ubiquitination method in which a phosphoribosyl ubiquitin (PR-Ub) is conjugated to a serine residue on substrates via a phosphodiester bond 6-8 . Here we present the crystal structure of a fragment of the SidE family member SdeA that retains ubiquitination activity, and determine the mechanism of this unique post-translational modification. The structure reveals that the catalytic module contains two distinct functional units: a phosphodiesterase domain and a mono-ADP-ribosyltransferase domain. Biochemical analysis shows that the mono-ADP-ribosyltransferase domain-mediated conversion of Ub to ADP-ribosylated Ub (ADPR-Ub) and the phosphodiesterase domain-mediated ligation of PR-Ub to substrates are two independent activities of SdeA. Furthermore, we present two crystal structures of a homologous phosphodiesterase domain from the SidE family member SdeD 9 in complexes with Ub and ADPR-Ub. The structures suggest a mechanism for how SdeA processes ADPR-Ub to PR-Ub and AMP, and conjugates PR-Ub to a serine residue in substrates. Our study establishes the molecular mechanism of phosphoribosyl-linked ubiquitination and will enable future studies of this unusual type of ubiquitination in eukaryotes.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.,Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA. ym253@cornell.edu.,Purdue Institute of Immunology, Inflammation and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SdeD (lpg2509) H67A
A
383Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Mutation(s): 1 
Find proteins for Q5ZSK8 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Go to UniProtKB:  Q5ZSK8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
B, C
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR6
Query on AR6

Download SDF File 
Download CCD File 
B
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.677α = 90.00
b = 58.768β = 114.42
c = 75.111γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM094347

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Data collection, Database references
  • Version 1.2: 2018-06-13
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection