› 3er9

X-ray diffraction
2.06Å resolution

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with UU and 3'-deoxy ATP

Released:
DOI: 10.2210/pdb3er9/pdb
PDB entry 3er9 coloured by chain, front view.
PDB entry 3er9 coloured by chain, side view.
PDB entry 3er9 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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139667 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase Chain: A
Molecule details ›
Chain: A
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 Chain: B
Molecule details ›
Chain: B
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:
5'-R(UP*U)-3' Chain: D
Molecule details ›
Chain: D
Length: 2 nucleotides
Theoretical weight: 567 Da

Ligands and Environments

3 bound ligands:
Ligand GOL 3 x GOL
Ligand 3AT 1 x 3AT
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P212121
Unit cell:
a: 69.531Å b: 91.977Å c: 133.734Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.208 0.25
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

1 mention without citation

Comparative molecular docking analysis of cytoplasmic dynein light chain DYNLL1 with pilin to explore the molecular mechanism of pathogenesis caused by Pseudomonas aeruginosa PAO.
Kausar et al. (2013)