PDBsum entry 7k0r

Viral protein

PDB id: 7k0r

Contents

Protein chains

(+ 0 more) 345 a.a.

Ligands

U5P ×6

PO4 ×6

PDB id:

7k0r

Name:

Viral protein

Title:

Nucleotide bound sars-cov-2 nsp15

Structure:

Uridylate-specific endoribonuclease. Chain: a, b, c, d, e, f. Synonym: nendou, non-structural protein 15, nsp15. Engineered: yes

Source:

Severe acute respiratory syndrome coronavirus 2. 2019-ncov. Organism_taxid: 2697049. Gene: rep, 1a-1b. Expressed in: escherichia coli. Expression_system_taxid: 562

Authors:

M.C.Pillon,R.E.Stanley

Key ref:

M.C.Pillon et al. (2021). Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics. Nat Commun, 12, 636. PubMed id: 33504779

Date:

04-Sep-20 Release date: 09-Dec-20

Protein chains

P0DTD1  (R1AB_SARS2) -

Enzyme reactions

• Enzyme class: E.C.3.1.-.-

Nat Commun 12:636 (2021)

PubMed id: 33504779

Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics.

M.C.Pillon, M.N.Frazier, L.B.Dillard, J.G.Williams, S.Kocaman, J.M.Krahn, L.Perera, C.K.Hayne, J.Gordon, Z.D.Stewart, M.Sobhany, L.J.Deterding, A.L.Hsu, V.P.Dandey, M.J.Borgnia, R.E.Stanley.

ABSTRACT

Nsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme recognizes and processes RNA remains poorly understood. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15, in both apo and UTP-bound states. The cryo-EM reconstructions, combined with biochemistry, mass spectrometry, and molecular dynamics, expose molecular details of how critical active site residues recognize uridine and facilitate catalysis of the phosphodiester bond. Mass spectrometry revealed the accumulation of cyclic phosphate cleavage products, while analysis of the apo and UTP-bound datasets revealed conformational dynamics not observed by crystal structures that are likely important to facilitate substrate recognition and regulate nuclease activity. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.