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J. Biol. Chem., Vol. 279, Issue 45, 47212-47221, November 5, 2004

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Structure of Foot-and-Mouth Disease Virus RNA-dependent RNA Polymerase and Its Complex with a Template-Primer RNA^*

Cristina Ferrer-Orta, Armando Arias¶||, Rosa Perez-Luque, Cristina Escarmís¶, Esteban Domingo¶, and Nuria Verdaguer**

From the Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Josep Samitier 1–5, E-08028 Barcelona, Spain and the ^¶Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain

Genome replication in picornaviruses is catalyzed by a virally encoded RNA-dependent RNA polymerase, termed 3D. The enzyme performs this operation, together with other viral and probably host proteins, in the cytoplasm of their host cells. The crystal structure of the 3D polymerase of foot-and-mouth disease virus, one of the most important animal pathogens, has been determined unliganded and bound to a template-primer RNA decanucleotide. The enzyme folds in the characteristic fingers, palm and thumb subdomains, with the presence of an NH₂-terminal segment that encircles the active site. In the complex, several conserved amino acid side chains bind to the template-primer, likely mediating the initiation of RNA synthesis. The structure provides essential information for studies on RNA replication and the design of antiviral compounds.

Received for publication, May 17, 2004 , and in revised form, August 2, 2004.

The atomic coordinates and structure factors (codes 1U09 and 1WNE) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported in part by Grants BMC2001-1823-C02-01 of Comisión Interministerial de Ciencia y Tecnología, Comunidad Autónoma de Madrid 08.2/0015/2001 and Fundación R. Areces (to E. D.) and Grant BIO2002-00517 of the Comisión Interministerial de Ciencia y Tecnología (to N. V.). Data were collected at the EMBL protein crystallography beam lines ID13 and ID29 at ESRF (Grenoble) within a Block Allocation Group (BAG Barcelona) with financial support provided by the ESRF. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Supported by a fellowship from the Ministerio de Ciencia y Tecnología.

^|| Supported by a fellowship from the Comunidad Autónoma de Madrid.

^** To whom correspondence should be addressed. Tel.: 34-93-403-49-52; Fax: 34-93-403-49-79; E-mail: nvmcri{at}ibmb.csic.es.

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