Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content

• Total Structure Weight: 60.59 kDa 
• Atom Count: 3949 
• Residue Count: 464 
• Unique protein chains: 2

6B7M

Crystal structure of Legionella effector sdeD (lpg2509) in complex with Ubiquitin

• DOI: 10.2210/pdb6B7M/pdb

• Classification: CELL INVASION
• Organism(s): Legionella pneumophila, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 1.70 Å
• R-Value Free: 0.196 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

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: 10.1038/s41586-018-0147-6
• Primary Citation of Related Structures:  
  6B7M, 6B7P, 6B7O, 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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SdeD (lpg2509)	A	383	Legionella pneumophila	Mutation(s): 0  Gene Names: lpg2509
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
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.196 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.765	α = 90
b = 58.593	β = 114.66
c = 74.124	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

• Deposited Date: 2017-10-04 
• 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