4RF1

Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P63)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression.

Bailey-Elkin, B.A.Knaap, R.C.Johnson, G.G.Dalebout, T.J.Ninaber, D.K.van Kasteren, P.B.Bredenbeek, P.J.Snijder, E.J.Kikkert, M.Mark, B.L.

(2014) J Biol Chem 289: 34667-34682

  • DOI: 10.1074/jbc.M114.609644
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human pathogen that was first isolated in 2012. MERS-CoV replication depends in part on a virus-encoded papain-like protease (PL(pro)) that cleaves the viral replicase polypr ...

    Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human pathogen that was first isolated in 2012. MERS-CoV replication depends in part on a virus-encoded papain-like protease (PL(pro)) that cleaves the viral replicase polyproteins at three sites releasing non-structural protein 1 (nsp1), nsp2, and nsp3. In addition to this replicative function, MERS-CoV PL(pro) was recently shown to be a deubiquitinating enzyme (DUB) and to possess deISGylating activity, as previously reported for other coronaviral PL(pro) domains, including that of severe acute respiratory syndrome coronavirus. These activities have been suggested to suppress host antiviral responses during infection. To understand the molecular basis for ubiquitin (Ub) recognition and deconjugation by MERS-CoV PL(pro), we determined its crystal structure in complex with Ub. Guided by this structure, mutations were introduced into PL(pro) to specifically disrupt Ub binding without affecting viral polyprotein cleavage, as determined using an in trans nsp3↓4 cleavage assay. Having developed a strategy to selectively disable PL(pro) DUB activity, we were able to specifically examine the effects of this activity on the innate immune response. Whereas the wild-type PL(pro) domain was found to suppress IFN-β promoter activation, PL(pro) variants specifically lacking DUB activity were no longer able to do so. These findings directly implicate the DUB function of PL(pro), and not its proteolytic activity per se, in the inhibition of IFN-β promoter activity. The ability to decouple the DUB activity of PL(pro) from its role in viral polyprotein processing now provides an approach to further dissect the role(s) of PL(pro) as a viral DUB during MERS-CoV infection.


    Organizational Affiliation

    From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and brian.mark@umanitoba.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORF1ab protein
A
324Human betacoronavirus 2c Jordan-N3/2012Mutation(s): 0 
Gene Names: ORF1ab
Find proteins for M4STU1 (Human betacoronavirus 2c Jordan-N3/2012)
Go to UniProtKB:  M4STU1
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
B
75Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
Find proteins for P62987 (Homo sapiens)
Go to UniProtKB:  P62987
NIH Common Fund Data Resources
PHAROS  P62987
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGO
Query on PGO

Download CCD File 
A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
3CN
Query on 3CN

Download CCD File 
B
3-AMINOPROPANE
C3 H9 N
WGYKZJWCGVVSQN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.77α = 90
b = 136.77β = 90
c = 57.991γ = 120
Software Package:
Software NamePurpose
MxDCdata collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Database references