The structure of a protein primer–polymerase complex in the initiation of genome replication

Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X-ray structure of two complexes between foot-and-mouth disease virus 3D, VPg1, the substrate UTP and divalent cations, in the absence and in the presence of an oligoadenylate of 10 residues. In both complexes, VPg fits the RNA binding cleft of the polymerase and projects the key residue Tyr3 into the active site of 3D. This is achieved by multiple interactions with residues of motif F and helix α8 of the fingers domain and helix α13 of the thumb domain of the polymerase. The complex obtained in the presence of the oligoadenylate showed the product of the VPg uridylylation (VPg-UMP). Two metal ions and the catalytic aspartic acids of the polymerase active site, together with the basic residues of motif F, have been identified as participating in the priming reaction. © 2006 European Molecular Biology Organization | All Rights Reserved.
Work in Barcelona was supported by Grants BIO2002-00517 and BFU2005-02376/BMC. Work in Madrid by Grants BMC 2001.1823.C02-01, BFU2005-00863/BMC and Fundación R Areces. CF and AA were supported by I3P fellowships from Ministerio de Educación y Ciencia. RA was supported by an FPI fellowship from Comunidad de Madrid. The financial support was provided by the ESRF