6K2U

Crystal structure of Thr66 ADP-ribosylated ubiquitin

• PDB DOI:  https://doi.org/10.2210/pdb6K2U/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-15 Released: 2020-03-18 
• Deposition Author(s): Wang, X., Zhou, Y., Zhu, Y.
• Funding Organization(s): National Natural Science Foundation of China, Ministry of Science and Technology (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.247 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Literature

Threonine ADP-Ribosylation of Ubiquitin by a Bacterial Effector Family Blocks Host Ubiquitination.

Yan, F., Huang, C., Wang, X., Tan, J., Cheng, S., Wan, M., Wang, Z., Wang, S., Luo, S., Li, A., Guo, X., Feng, M., Liu, X., Zhu, Y., Zhou, Y.

(2020) Mol Cell 78: 641-652.e9

• PubMed: 32330457 
• DOI: https://doi.org/10.1016/j.molcel.2020.03.016
• Primary Citation of Related Structures:  
  6K2U


• PubMed Abstract: 
  

Ubiquitination is essential for numerous eukaryotic cellular processes. Here, we show that the type III effector CteC from Chromobacterium violaceum functions as an adenosine diphosphate (ADP)-ribosyltransferase that specifically modifies ubiquitin via threonine ADP-ribosylation on residue T66. The covalent modification prevents the transfer of ubiquitin from ubiquitin-activating enzyme E1 to ubiquitin-conjugating enzyme E2, which inhibits subsequent ubiquitin activation by E2 and E3 enzymes in the ubiquitination cascade and leads to the shutdown of polyubiquitin synthesis in host cells. This unique modification also causes dysfunction of polyubiquitin chains in cells, thereby blocking host ubiquitin signaling. The disruption of host ubiquitination by CteC plays a crucial role in C. violaceum colonization in mice during infection. CteC represents a family of effector proteins in pathogens of hosts from different kingdoms. All the members of this family specifically ADP-ribosylate ubiquitin. The action of CteC reveals a new mechanism for interfering with host ubiquitination by pathogens.

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Organizational Affiliation: 

Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 9.34 kDa 
• Atom Count: 626 
• Modelled Residue Count: 73 
• Deposited Residue Count: 77 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	A [auth B]	77	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR (Subject of Investigation/LOI)	B	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.247 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.525	α = 90
b = 101.525	β = 90
c = 101.525	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Wang, X., Zhou, Y., Zhu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81530068
National Natural Science Foundation of China	China	81322024
National Natural Science Foundation of China	China	31370722
National Natural Science Foundation of China	China	81561130162
National Natural Science Foundation of China	China	81501717
Ministry of Science and Technology (China)	China	2017YFA0503900

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 2.0: 2023-04-05
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary