2z3d

X-ray diffraction
2.1Å resolution

A Mechanistic view of Enzyme Inhibition and Peptide Hydrolysis in the Active Site of the SARS-CoV 3C-Like peptidase

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:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-143117 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
3C-like proteinase nsp5 Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 33.88 KDa
Source organism: Severe acute respiratory syndrome-related coronavirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C6X7 (Residues: 3241-3546; Coverage: 4%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus endopeptidase C30
Structure domains:
Inhibitor Chain: I
Molecule details ›
Chain: I
Length: 5 amino acids
Theoretical weight: 454 Da
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: C2
Unit cell:
a: 108.226Å b: 81.836Å c: 53.425Å
α: 90° β: 104.17° γ: 90°
R-values:
R R work R free
0.201 0.198 0.248
Expression systems:
  • Escherichia coli
  • Not provided