6BI8

X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease.

Clasman, J.R.Everett, R.K.Srinivasan, K.Mesecar, A.D.

(2020) Antiviral Res 174: 104661-104661

  • DOI: https://doi.org/10.1016/j.antiviral.2019.104661
  • Primary Citation of Related Structures:  
    6BI8

  • PubMed Abstract: 

    Coronavirus papain-like proteases (PLPs or PLpro), such as the one encoded in the genome of the infectious Middle East Respiratory Syndrome (MERS) virus, have multiple enzymatic activities that promote viral infection. PLpro acts as a protease and processes the large coronavirus polyprotein for virus replication. PLpro also functions as both a deubiquitinating (DUB) and deISGylating (deISG) enzyme and removes ubiquitin (Ub) and interferon-stimulated gene 15 (ISG15) from cellular proteins. Both DUB and deISG activities are implicated in suppressing innate immune responses; however, the precise role of each activity in this process is still unclear due in part to the difficulties in separating each activity. In this study, we determine the first structure of MERS PLpro in complex with the full-length human ISG15 to a resolution of 2.3 Å. This structure and available structures of MERS PLpro-Ub complexes were used as molecular guides to design PLpro mutants that lack either or both DUB/deISG activities. We tested 13 different PLpro mutants for protease, DUB, and deISG activitites using fluorescence-based assays. Results show that we can selectively modulate DUB activity at amino acid positions 1649 and 1653 while mutation of Val1691 or His1652 of PLpro to a positive charged residue completely impairs both DUB/deISG activities. These mutant enzymes will provide new functional tools for delineating the importance of DUB versus deISG activity in virus-infected cells and may serve as potential candidates for attenuating the MERS virus in vivo for modified vaccine design efforts.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF1a
A, B
259Human betacoronavirus 2c EMC/2012Mutation(s): 0 
Gene Names: orf1ab
UniProt
Find proteins for K0BWD0 (Human betacoronavirus 2c EMC/2012)
Explore K0BWD0 
Go to UniProtKB:  K0BWD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK0BWD0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein ISG15
C, D
156Homo sapiensMutation(s): 1 
Gene Names: ISG15G1P2UCRP
UniProt & NIH Common Fund Data Resources
Find proteins for P05161 (Homo sapiens)
Explore P05161 
Go to UniProtKB:  P05161
PHAROS:  P05161
GTEx:  ENSG00000187608 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05161
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
P [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
K [auth B],
T [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
AYE
Query on AYE

Download Ideal Coordinates CCD File 
I [auth A],
S [auth B]
prop-2-en-1-amine
C3 H7 N
VVJKKWFAADXIJK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.035α = 90
b = 148.035β = 90
c = 134.189γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI085089
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA023168
MEDCUnited States085P1000817

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-11-27
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2020-05-20
    Changes: Database references
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description