5E6J

Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe

  • Classification: HYDROLASE
  • Organism(s): Human SARS coronavirus, Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2015-10-09 Released: 2016-05-18 
  • Deposition Author(s): Lima, C.D., Bekes, M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); Howard Hughes Medical Institute (HHMI); Netherlands Organisation for Scientific Research (NWO) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 

Literature

Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease.

Bekes, M., van der Heden van Noort, G.J., Ekkebus, R., Ovaa, H., Huang, T.T., Lima, C.D.

(2016) Mol. Cell 62: 572-585

  • DOI: 10.1016/j.molcel.2016.04.016

  • PubMed Abstract: 

    • Deubiquitinating enzymes (DUBs) recognize and cleave linkage-specific polyubiquitin (polyUb) chains, but mechanisms underlying specificity remain elusive in many cases. The severe acute respiratory syndrome (SARS) coronavirus papain-like protease (PL ...

    Deubiquitinating enzymes (DUBs) recognize and cleave linkage-specific polyubiquitin (polyUb) chains, but mechanisms underlying specificity remain elusive in many cases. The severe acute respiratory syndrome (SARS) coronavirus papain-like protease (PLpro) is a DUB that cleaves ISG15, a two-domain Ub-like protein, and Lys48-linked polyUb chains, releasing diUb(Lys48) products. To elucidate this specificity, we report the 2.85 Å crystal structure of SARS PLpro bound to a diUb(Lys48) activity-based probe. SARS PLpro binds diUb(Lys48) in an extended conformation via two contact sites, S1 and S2, which are proximal and distal to the active site, respectively. We show that specificity for polyUb(Lys48) chains is predicated on contacts in the S2 site and enhanced by an S1-S1' preference for a Lys48 linkage across the active site. In contrast, ISG15 specificity is dominated by contacts in the S1 site. Determinants revealed for polyUb(Lys48) specificity should prove useful in understanding PLpro deubiquitinating activities in coronavirus infections.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA. Electronic address: tony.huang@nyumc.org.,Division of Cell Biology II, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.,Division of Cell Biology II, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Electronic address: h.ovaa@nki.nl.,Structural Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA. Electronic address: limac@mskcc.org.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Structural Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicase polyprotein 1ab
A, D
325Human SARS coronavirusMutation(s): 0 
Gene Names: rep
Find proteins for P0C6X7 (Human SARS coronavirus)
Go to UniProtKB:  P0C6X7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ubiquitin
B, E
76Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
C, F
75Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NI
Query on NI
Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
5MW
Query on 5MW
B, E
L-peptide linkingC8 H15 N5 O2LYS
AYE
Query on AYE
B, E
NON-POLYMERC3 H7 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.981α = 90.00
b = 68.239β = 103.21
c = 119.021γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-10-09 
  • Released Date: 2016-05-18 
  • Deposition Author(s): Lima, C.D., Bekes, M.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM065872
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM100598
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM084244
Howard Hughes Medical Institute (HHMI)United States--
Netherlands Organisation for Scientific Research (NWO)Netherlands724013002

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Derived calculations
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence
  • Version 1.3: 2017-11-01
    Type: Author supporting evidence
  • Version 1.4: 2017-12-20
    Type: Database references
  • Version 1.5: 2019-11-20
    Type: Author supporting evidence