4RNA | pdb_00004rna

Crystal structure of PLpro from Middle East Respiratory Syndrome (MERS) coronavirus

• PDB DOI: https://doi.org/10.2210/pdb4RNA/pdb

• Classification: HYDROLASE
• Organism(s): Human betacoronavirus 2c EMC/2012
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-10-23 Released: 2015-03-25 
• Deposition Author(s): Lei, H., Santarsiero, B.D., Lee, H., Johnson, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Inhibitor Recognition Specificity of MERS-CoV Papain-like Protease May Differ from That of SARS-CoV.

Lee, H., Lei, H., Santarsiero, B.D., Gatuz, J.L., Cao, S., Rice, A.J., Patel, K., Szypulinski, M.Z., Ojeda, I., Ghosh, A.K., Johnson, M.E.

(2015) ACS Chem Biol 10: 1456-1465

• PubMed: 25746232 
• DOI: https://doi.org/10.1021/cb500917m
• Primary Citation Related Structures: 
  4RNA


• PubMed Abstract: 
  

  The Middle East Respiratory Syndrome coronavirus (MERS-CoV) papain-like protease (PLpro) blocking loop 2 (BL2) structure differs significantly from that of SARS-CoV PLpro, where it has been proven to play a crucial role in SARS-CoV PLpro inhibitor binding. Four SARS-CoV PLpro lead inhibitors were tested against MERS-CoV PLpro, none of which were effective against MERS-CoV PLpro. Structure and sequence alignments revealed that two residues, Y269 and Q270, responsible for inhibitor binding to SARS-CoV PLpro, were replaced by T274 and A275 in MERS-CoV PLpro, making critical binding interactions difficult to form for similar types of inhibitors. High-throughput screening (HTS) of 25 000 compounds against both PLpro enzymes identified a small fragment-like noncovalent dual inhibitor. Mode of inhibition studies by enzyme kinetics and competition surface plasmon resonance (SPR) analyses suggested that this compound acts as a competitive inhibitor with an IC50 of 6 μM against MERS-CoV PLpro, indicating that it binds to the active site, whereas it acts as an allosteric inhibitor against SARS-CoV PLpro with an IC50 of 11 μM. These results raised the possibility that inhibitor recognition specificity of MERS-CoV PLpro may differ from that of SARS-CoV PLpro. In addition, inhibitory activity of this compound was selective for SARS-CoV and MERS-CoV PLpro enzymes over two human homologues, the ubiquitin C-terminal hydrolases 1 and 3 (hUCH-L1 and hUCH-L3).

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Organizational Affiliation: 
• †Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States.
‡Departments of Chemistry and Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 36.5 kDa 
• Atom Count: 2,745 
• Modeled Residue Count: 321 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
papain-like protease	A	324	Human betacoronavirus 2c EMC/2012	Mutation(s): 0  Gene Names: orf1ab EC: 3.4.22
UniProt
Find proteins for K4LC41 (Human betacoronavirus 2c (isolate EMC/2012)) Explore K4LC41  Go to UniProtKB:  K4LC41

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.899	α = 90
b = 48.78	β = 121.52
c = 87.464	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Lei, H., Santarsiero, B.D., Lee, H., Johnson, M.E.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2015-07-01
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection