6WLC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


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

  • DOI: 10.1038/s42003-021-01735-9
  • Primary Citation of Related Structures:  
    7K1L, 6X4I, 6WXC, 6WLC, 6X1B

  • 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 ...

    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.


    Related Citations: 
    • 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,, N., Randall, G., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
      (2020) Biorxiv --: --

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA. andrzejj@anl.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uridylate-specific endoribonucleaseA, B370Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.1 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U5P (Subject of Investigation/LOI)
Query on U5P

Download Ideal Coordinates CCD File 
C [auth A], M [auth B]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A], N [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , O [auth B] , P [auth B] , 
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
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A], Q [auth B], S [auth B], T [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
U [auth B], V [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 63
  • Diffraction Data DOI: 10.18430/m36wlc Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.957α = 90
b = 150.957β = 90
c = 112.304γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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