A picornaviral loop-to-loop replication complex.
Picornaviruses replicate their RNA genomes through a highly conserved mechanism that involves an interaction between the principal viral protease (3C(pro)) and the 5'-UTR region of the viral genome. The 3C(pro) catalytic site is the target of numerous replication inhibitors. This paper describes the first structural model of a complex between a picornaviral 3C(pro) and a region of the 5'-UTR, stem-loop D (SLD). Using human rhinovirus as a model system, we have combined NMR contact information, small-angle X-ray scattering (SAXS) data, and previous mutagenesis results to determine the shape, position and relative orientation of the 3C(pro) and SLD components. The results clearly identify a 1:1 binding stoichiometry, with pronounced loops from each molecule providing the key binding determinants for the interaction. Binding between SLD and 3C(pro) induces structural changes in the proteolytic active site that is positioned on the opposite side of the protease relative to the RNA/protein interface, suggesting that subtle conformational changes affecting catalytic activity are relayed through the protein.
Claridge
Jolyon K
JK
Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
Headey
Stephen J
SJ
Chow
John Y H
JY
Schwalbe
Martin
M
Edwards
Patrick J
PJ
Jeffries
Cy M
CM
Venugopal
Hariprasad
H
Trewhella
Jill
J
Pascal
Steven M
SM
D000086042:3C Viral Proteases; D020121:5' Untranslated Regions / Q000235:genetics*; D003546:Cysteine Endopeptidases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016679:Genome, Viral / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D016296:Mutagenesis; D010849:Picornaviridae / Q000235:genetics*; D017433:Protein Structure, Secondary; D012229:Rhinovirus / Q000235:genetics; D053838:Scattering, Small Angle; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014779:Virus Replication / Q000235:genetics*; D014961:X-Ray Diffraction / Q000379:methods
D020121:5' Untranslated Regions; D014764:Viral Proteins; D003546:Cysteine Endopeptidases; D000086042:3C Viral Proteases