6WLC | pdb_00006wlc

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-5'-Monophosphate

• PDB DOI: https://doi.org/10.2210/pdb6WLC/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-19 Released: 2020-04-29 
• Deposition Author(s): Kim, Y., Maltseva, N., Jedrzejczak, R., Endres, M., Chang, C., Godzik, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.195 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.

Kim, Y., Wower, J., Maltseva, N., Chang, C., Jedrzejczak, R., Wilamowski, M., Kang, S., Nicolaescu, V., Randall, G., Michalska, K., Joachimiak, A.

(2021) Commun Biol 4: 193-193

• PubMed: 33564093 
• DOI: https://doi.org/10.1038/s42003-021-01735-9
• Primary Citation Related Structures: 
  6WLC, 6WXC, 6X1B, 6X4I, 7K1L


• PubMed Abstract: 
  

  SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family that is highly conserved in coronaviruses. As endoribonuclease activity seems to be responsible for the interference with the innate immune response, Nsp15 emerges as an attractive target for therapeutic intervention. Here we report the first structures with bound nucleotides and show how the enzyme specifically recognizes uridine moiety. In addition to a uridine site we present evidence for a second base binding site that can accommodate any base. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. This acquired knowledge was instrumental in identifying Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. Using crystallography, biochemical, and whole-cell assays, we demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme's active site. Our findings provide new insights for the development of uracil scaffold-based drugs.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
Department of Animal Sciences, Auburn University, Auburn, AL, 36849, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA.
Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, 60367, USA.
Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA. [e-mail].
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. [e-mail].
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 85.25 kDa 
• Atom Count: 6,318 
• Modeled Residue Count: 696 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate-specific endoribonuclease	A, B	370	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.1
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P (Subject of Investigation/LOI)	C [auth A], M [auth B]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
TRS	D [auth A], N [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], R [auth B], W [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	F [auth A], Q [auth B], S [auth B], T [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	U [auth B], V [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.195 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36wlc

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.957	α = 90
b = 150.957	β = 90
c = 112.304	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Kim, Y., Maltseva, N., Jedrzejczak, R., Endres, M., Chang, C., Godzik, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.0: 2020-06-10
  Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2020-12-09
  Changes: Database references
• Version 2.2: 2021-02-24
  Changes: Database references
• Version 2.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description