› 3erc

X-ray diffraction
3.21Å resolution

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP

Released:
DOI: 10.2210/pdb3erc/pdb
PDB entry 3erc coloured by chain, front view.
PDB entry 3erc coloured by chain, side view.
PDB entry 3erc coloured by chain, top view.
Source organism: Vaccinia virus WR
Primary publication:
Polymerase translocation with respect to single-stranded nucleic acid: looping or wrapping of primer around a poly(A) polymerase.
Li C, Li H, Zhou S, Sun E, Yoshizawa J, Poulos TL, Gershon PD
Structure 17 680-9 (2009)
PMID: 19446524

Function and Biology Details

Reactions catalysed: 
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]
ATP + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139668 (preferred)
Entry contents:
2 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (5 distinct):
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 297 amino acids
Theoretical weight: 34.59 KDa
Source organism: Vaccinia virus WR
Expression system: Escherichia coli
UniProt:
  • Canonical: P07617 (Residues: 1-297; Coverage: 89%)
Gene names: J3R, OPG102, PAPS, VACWR095
Sequence domains: Poly A polymerase regulatory subunit
Structure domains: Vaccinia Virus protein VP39
Poly(A) polymerase catalytic subunit Chains: C, D
Molecule details ›
Chains: C, D
Length: 479 amino acids
Theoretical weight: 55.57 KDa
Source organism: Vaccinia virus WR
Expression system: Escherichia coli
UniProt:
  • Canonical: P23371 (Residues: 1-479; Coverage: 100%)
Gene names: E1L, OPG063, PAPL, VACWR057
Sequence domains:
Structure domains:
RNA/DNA chimera (5'-D(CP*)R(UP*UP*)D(CP*C)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 5 nucleotides
Theoretical weight: 1.43 KDa
RNA/DNA chimera (5'-D(CP*)R(UP*UP*)-D(C)-3') Chain: G
Molecule details ›
Chain: G
Length: 4 nucleotides
Theoretical weight: 1.15 KDa
RNA/DNA chimera (5'-D(CP*CP*)R(UP*UP*)D(C)-3') Chain: I
Molecule details ›
Chain: I
Length: 5 nucleotides
Theoretical weight: 1.43 KDa

Ligands and Environments

3 bound ligands:
Ligand U 2 x U
Ligand 3AT 2 x 3AT
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P1
Unit cell:
a: 69.925Å b: 77.153Å c: 108.03Å
α: 89.52° β: 73.45° γ: 63.76°
R-values:
R R work R free
0.245 0.245 0.309
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Investigations of Single-Subunit tRNA Methyltransferases from Yeast.
Wang et al. (2023)
1 other article

3 mentions without citation

mRNA maturation in giant viruses: variation on a theme.
Priet et al. (2015)
2 more