6X1B

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 2.4 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:  
    6WLC, 6X1B, 6X4I, 6WXC, 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 im ...

    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 endoribonuclease A, B370Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep, 1a-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)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-R(*GP*U)-3')D, F2synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.97 Å
    • R-Value Free: 0.185 
    • R-Value Work: 0.157 
    • R-Value Observed: 0.165 
    • Space Group: P 63
    • Diffraction Data DOI: 10.18430/m36x1b Protein Diffraction
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 150.875α = 90
    b = 150.875β = 90
    c = 111.73γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-3000data reduction
    HKL-3000data scaling
    HKL-3000phasing
    MOLREPphasing
    Cootmodel building

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    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 

    • Version 1.0: 2020-05-27
      Type: Initial release
    • Version 2.0: 2020-06-10
      Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
    • Version 2.1: 2020-08-05
      Changes: Database references, Structure summary
    • Version 2.2: 2020-12-09
      Changes: Database references
    • Version 2.3: 2021-01-27
      Changes: Structure summary
    • Version 2.4: 2021-02-24
      Changes: Database references