6B7O | pdb_00006b7o

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

• PDB DOI: https://doi.org/10.2210/pdb6B7O/pdb

• Classification: CELL INVASION
• Organism(s): Legionella pneumophila, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-10-04 Released: 2018-04-18 
• Deposition Author(s): Mao, Y., Akturk, A., Wasilko, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.159 (Depositor) 
• R-Value Observed: 
  0.161 (Depositor) 

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

• PubMed: 29795346 
• DOI: https://doi.org/10.1038/s41586-018-0147-6
• Primary Citation Related Structures: 
  6B7M, 6B7O, 6B7P, 6B7Q


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
Purdue Institute of Immunology, Inflammation and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content 

• Total Structure Weight: 61.08 kDa 
• Atom Count: 3,976 
• Modeled Residue Count: 465 
• Deposited Residue Count: 535 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SdeD (lpg2509) H67A	A	383	Legionella pneumophila	Mutation(s): 1  Gene Names: lpg2509
UniProt
Find proteins for Q5ZSK8 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSK8  Go to UniProtKB:  Q5ZSK8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	B, C	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6	D [auth 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.159 (Depositor) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.677	α = 90
b = 58.768	β = 114.42
c = 75.111	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Mao, Y., Akturk, A., Wasilko, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM094347

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2018-06-06
  Changes: Data collection, Database references
• Version 1.2: 2018-06-13
  Changes: Data collection, Database references
• Version 1.3: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary