2CKW

The 2.3 A resolution structure of the Sapporo virus RNA dependant RNA polymerase.

Summary for 2CKW

• Entry DOI: 10.2210/pdb2ckw/pdb
• Descriptor: RNA-DIRECTED RNA POLYMERASE (2 entities in total)
• Functional Keywords: hydrolase, nucleotide-binding, nucleotidyltransferase, covalent protein-rna linkage, polymerase, rna elongation, transferase activity, mutant, capsid protein, rna replication, structural protein, protease, helicase, transferase, rna-directed rna polymerase, polyprotein, atp-binding, thiol protease
• Biological source: SAPPORO VIRUS
• Total number of polymer chains: 1
• Total formula weight: 56485.71

Authors

Fullerton, S.W.B.,Tucker, P.A.,Rohayem, J.,Coutard, B.,Gebhardt, J.,Gorbalenya, A.,Canard, B. (deposition date: 2006-04-24, release date: 2006-11-29, Last modification date: 2023-12-13)

Primary citation

Fullerton, S.W.B.,Blaschke, M.,Coutard, B.,Gebhardt, J.,Gorbalenya, A.,Canard, B.,Tucker, P.A.,Rohayem, J.
Structural and Functional Characterization of Sapovirus RNA-Dependent RNA Polymerase.
J.Virol., 81:1858-, 2007

PubMed Abstract: Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the Caliciviridae family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3D(pol)-like protein. Enzymatically active sapovirus 3D(pol) and its defective mutant were expressed in Escherichia coli and purified. The overall structure of the sapovirus 3D(pol) was determined by X-ray crystallography to 2.32-A resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3D(pol) prefers Mn(2+) over Mg(2+) but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3D(pol) synthesizes a double-stranded RNA or labels the template 3' terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3D(pol) an attractive target for developing drugs to control calicivirus infection in humans.

PubMed: 17121797
DOI: 10.1128/JVI.01462-06

Experimental method

X-RAY DIFFRACTION (2.3 Å)