8EHO | pdb_00008eho

PRRSV-1 PLP2 domain bound to ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb8EHO/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Porcine reproductive and respiratory syndrome virus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-14 Released: 2023-12-06 
• Deposition Author(s): Bailey-Elkin, B.A., Mark, B.L.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.247 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Demonstrating the importance of porcine reproductive and respiratory syndrome virus papain-like protease 2 deubiquitinating activity in viral replication by structure-guided mutagenesis.

Bailey-Elkin, B.A., Knaap, R.C.M., De Silva, A., Boekhoud, I.M., Mous, S., van Vught, N., Khajehpour, M., van den Born, E., Kikkert, M., Mark, B.L.

(2023) PLoS Pathog 19: e1011872-e1011872

• PubMed: 38096325 
• DOI: https://doi.org/10.1371/journal.ppat.1011872
• Primary Citation Related Structures: 
  8EHN, 8EHO


• PubMed Abstract: 
  

  Deubiquitination of cellular substrates by viral proteases is a mechanism used to interfere with host cellular signaling processes, shared between members of the coronavirus- and arterivirus families. In the case of Arteriviruses, deubiquitinating and polyprotein processing activities are accomplished by the virus-encoded papain-like protease 2 (PLP2). Several studies have implicated the deubiquitinating activity of the porcine reproductive and respiratory syndrome virus (PRRSV) PLP2 in the downregulation of cellular interferon production, however to date, the only arterivirus PLP2 structure described is that of equine arteritis virus (EAV), a distantly related virus. Here we describe the first crystal structure of the PRRSV PLP2 domain both in the presence and absence of its ubiquitin substrate, which reveals unique structural differences in this viral domain compared to PLP2 from EAV. To probe the role of PRRSV PLP2 deubiquitinating activity in host immune evasion, we selectively removed this activity from the domain by mutagenesis and found that the viral domain could no longer downregulate cellular interferon production. Interestingly, unlike EAV, and also unlike the situation for MERS-CoV, we found that recombinant PRRSV carrying PLP2 DUB-specific mutations faces significant selective pressure to revert to wild-type virus in MARC-145 cells, suggesting that the PLP2 DUB activity, which in PRRSV is present as three different versions of viral protein nsp2 expressed during infection, is critically important for PRRSV replication.

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Organizational Affiliation: 
• Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, The Netherlands.
Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
MSD Animal Health, Boxmeer, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 92.84 kDa 
• Atom Count: 5,810 
• Modeled Residue Count: 721 
• Deposited Residue Count: 837 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease 2	A, C, E	204	Porcine reproductive and respiratory syndrome virus	Mutation(s): 0
UniProt
Find proteins for W0NX70 (Porcine reproductive and respiratory syndrome virus) Explore W0NX70  Go to UniProtKB:  W0NX70

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, D, F	75	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth A], I [auth A], M [auth C], N [auth C], P [auth D], R [auth E], S [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A], L [auth C], Q [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NO3	K [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
3CN	J [auth B], O [auth D], T [auth F]	3-AMINOPROPANE C3 H9 N WGYKZJWCGVVSQN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.247 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.686	α = 90
b = 159.492	β = 90
c = 147.325	γ = 90

Software Package:

Software Name	Purpose
PDB-REDO	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Bailey-Elkin, B.A., Mark, B.L.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPAS-2020-00012
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2020-05682

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release
  
• Version 1.1: 2024-01-03
  Changes: Database references
• Version 1.2: 2026-03-04
  Changes: Derived calculations, Refinement description, Structure summary