6S2L

FMDV 3D polymerase crystallized in presence of (F)uridylylated VPg peptide

Summary for 6S2L

• Entry DOI: 10.2210/pdb6s2l/pdb
• Related: 1U09 2D7S 2F8E
• Descriptor: Genome polyprotein, GLYCEROL (3 entities in total)
• Functional Keywords: rna dependent rna polymerase 3d polymerase vpg picornavirus, viral protein
• Biological source: Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C) (FMDV)
• Total number of polymer chains: 1
• Total formula weight: 54386.62

Authors

Verdaguer, N.,Ferrer-Orta, C. (deposition date: 2019-06-21, release date: 2019-07-03, Last modification date: 2024-01-24)

Primary citation

de Castro, S.,Ferrer-Orta, C.,Mills, A.,Fernandez-Cureses, G.,Gago, F.,Verdaguer, N.,Camarasa, M.J.
(F)uridylylated Peptides Linked to VPg1 of Foot-and- Mouth Disease Virus (FMDV): Design, Synthesis and X-Ray Crystallography of the Complexes with FMDV RNA-Dependent RNA Polymerase.
Molecules, 24:-, 2019

PubMed Abstract: Foot-and-mouth disease virus (FMDV) is an RNA virus belonging to the family that contains three small viral proteins (VPgs), named VPg1, VPg2 and VPg3, linked to the 5'-end of the viral genome. These VPg proteins act as primers for RNA replication, which is initiated by the consecutive binding of two UMP molecules to the hydroxyl group of Tyr3 in VPg. This process, termed uridylylation, is catalyzed by the viral RNA-dependent RNA polymerase named 3D. 5-Fluorouridine triphosphate (FUTP) is a potent competitive inhibitor of VPg uridylylation. Peptide analysis showed FUMP covalently linked to the Tyr3 of VPg. This fluorouridylylation prevents further incorporation of the second UMP residue. The molecular basis of how the incorporated FUMP blocks the incorporation of the second UMP is still unknown. To investigate the mechanism of inhibition of VPg uridylylation by FUMP, we have prepared a simplified 15-mer model of VPg1 containing FUMP and studied its x-ray crystal structure in complex with 3D. Unfortunately, the fluorouridylylated VPg1 was disordered and not visible in the electron density maps; however, the structure of 3D in the presence of VPg1-FUMP showed an 8 Å movement of the β9-α11 loop of the polymerase towards the active site cavity relative to the complex of 3D with VPg1-UMP. The conformational rearrangement of this loop preceding the 3D B motif seems to block the access of the template nucleotide to the catalytic cavity. This result may be useful in the design of new antivirals against not only FMDV but also other picornaviruses, since all members of this family require the uridylylation of their VPg proteins to initiate the viral RNA synthesis.

PubMed: 31247979
DOI: 10.3390/molecules24132360

Experimental method

X-RAY DIFFRACTION (2.3 Å)