› 1r6a

X-ray diffraction
2.6Å resolution

Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl homocysteine and ribavirin 5' triphosphate

Released:
DOI: 10.2210/pdb1r6a/pdb
PDB entry 1r6a coloured by chain, front view.
PDB entry 1r6a coloured by chain, side view.
PDB entry 1r6a coloured by chain, top view.
Source organism: Dengue virus 2 Puerto Rico/PR159-S1/1969
Primary publication:
A structural basis for the inhibition of the NS5 dengue virus mRNA 2'-O-methyltransferase domain by ribavirin 5'-triphosphate.
Benarroch D, Egloff MP, Mulard L, Guerreiro C, Romette JL, Canard B
J Biol Chem 279 35638-43 (2004)
PMID: 15152003

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)
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-146327 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA-directed RNA polymerase NS5 Chain: A
Molecule details ›
Chain: A
Length: 295 amino acids
Theoretical weight: 33.15 KDa
Source organism: Dengue virus 2 Puerto Rico/PR159-S1/1969
Expression system: Escherichia coli
UniProt:
  • Canonical: P12823 (Residues: 2492-2784; Coverage: 9%)
Sequence domains: FtsJ-like methyltransferase
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
2 bound ligands:
Ligand SO4 7 x SO4
Ligand RVP 1 x RVP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P3121
Unit cell:
a: 111.99Å b: 111.99Å c: 56.27Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.218 0.218 0.243
Expression system: Escherichia coli

Quick links

Citations

24 review citations

Mechanisms of action of ribavirin against distinct viruses.
Graci et al. (2006)
23 more

19 mentions without citation

RNA methyltransferases involved in 5' cap biosynthesis.
Byszewska et al. (2014)
18 more