Summary information and primary citation

PDB-id
3bsn; SNAP-derived features in text and JSON formats; DNAproDB
Class
transferase-RNA
Method
X-ray (1.8 Å)
Summary
Norwalk virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA
Reference
Zamyatkin DF, Parra F, Alonso JM, Harki DA, Peterson BR, Grochulski P, Ng KK (2008): "Structural insights into mechanisms of catalysis and inhibition in norwalk virus polymerase." J.Biol.Chem., 283, 7705-7712. doi: 10.1074/jbc.M709563200.
Abstract
Crystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex and either the natural substrate CTP or the inhibitor 5-nitrocytidine triphosphate have been determined to 1.8A resolution. These structures reveal a closed conformation of the polymerase that differs significantly from previously determined open structures of calicivirus and picornavirus polymerases. These closed complexes are trapped immediately prior to the nucleotidyl transfer reaction, with the triphosphate group of the nucleotide bound to two manganese ions at the active site, poised for reaction to the 3'-hydroxyl group of the RNA primer. The positioning of the 5-nitrocytidine triphosphate nitro group between the alpha-phosphate and the 3'-hydroxyl group of the primer suggests a novel, general approach for the design of antiviral compounds mimicking natural nucleosides and nucleotides.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js