6wlc

X-ray diffraction
1.82Å resolution

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

Released:

Function and Biology Details

Reactions catalysed:
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
ATP + H(2)O = ADP + phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
PDBe Complex ID:
PDB-CPX-145108 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridylate-specific endoribonuclease nsp15 Chains: A, B
Molecule details ›
Chains: A, B
Length: 370 amino acids
Theoretical weight: 41.66 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 6453-6798; Coverage: 5%)
Gene names: 1a-1b, rep
Sequence domains:

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P63
Unit cell:
a: 150.957Å b: 150.957Å c: 112.304Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.17 0.195
Expression system: Escherichia coli BL21(DE3)