› 5wfi

X-ray diffraction
1.85Å resolution

X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin

Released:
DOI: 10.2210/pdb5wfi/pdb
PDB entry 5wfi coloured by chain, front view.
PDB entry 5wfi coloured by chain, side view.
PDB entry 5wfi coloured by chain, top view.
Source organisms:
Entry authors: Mesecar AD, Chen Y

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).
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143130 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Papain-like proteinase nsp3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 303 amino acids
Theoretical weight: 33.89 KDa
Source organism: Murine hepatitis virus strain A59
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C6X9 (Residues: 1609-1911; Coverage: 4%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus papain-like peptidase
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

3 bound ligands:
Ligand GOL 10 x GOL
Ligand FMT 2 x FMT
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: C2
Unit cell:
a: 199.515Å b: 43.388Å c: 110.159Å
α: 90° β: 114.85° γ: 90°
R-values:
R R work R free
0.158 0.157 0.197
Expression systems:
  • Escherichia coli
  • Escherichia coli K-12

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