NMR solution structure of poliovirus uridylyated peptide linked to the genome (VPgpU)

Peptides. 2010 Aug;31(8):1441-8. doi: 10.1016/j.peptides.2010.04.021. Epub 2010 May 2.


Picornaviruses have a 22-24 amino acid peptide, VPg, bound covalently at the 5' end of their RNA, that is essential for replication. VPgs are uridylylated at a conserved tyrosine to form VPgpU, the primer of RNA synthesis by the viral polymerase. This first complete structure for any uridylylated VPg, of poliovirus type 1 (PV1)-VPgpU, shows that conserved amino acids in VPg stabilize the bound UMP, with the uridine atoms involved in base pairing and chain elongation projected outward. Comparing this structure to PV1-VPg and partial structures of VPg/VPgpU from other picornaviruses suggests that enteroviral polymerases require a more stable VPg structure than does the distantly related aphthovirus, foot and mouth disease virus (FMDV). The glutamine residue at the C-terminus of PV1-VPgpU lies in back of the uridine base and may stabilize its position during chain elongation and/or contribute to base specificity. Under in vivo-like conditions with the authentic cre(2C) hairpin RNA and Mg(2+), 5-methylUTP cannot compete with UTP for VPg uridylyation in an in vitro uridylyation assay, but both nucleotides are equally incorporated by PV1-polymerase with Mn(2+) and a poly-A RNA template. This indicates the 5 position is recognized under in vivo conditions. The compact VPgpU structure docks within the active site cavity of the PV-polymerase, close to the position seen for the fragment of FMDV-VPgpU with its polymerase. This structure could aid in design of novel enterovirus inhibitors, and stabilization upon uridylylation may also be pertinent for post-translational uridylylation reactions that underlie other biological processes.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Antiviral Agents / chemistry
  • Binding, Competitive
  • Drug Design
  • HeLa Cells
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Peptides / chemistry*
  • Peptides / metabolism*
  • Poliovirus / growth & development
  • Poliovirus / physiology*
  • Protein Conformation
  • Protein Processing, Post-Translational
  • Protein Stability
  • RNA-Dependent RNA Polymerase / chemistry
  • RNA-Dependent RNA Polymerase / metabolism
  • Sequence Alignment
  • Substrate Specificity
  • Uracil Nucleotides / chemistry*
  • Uracil Nucleotides / metabolism
  • Uridine Monophosphate / chemistry
  • Uridine Monophosphate / metabolism
  • Uridine Triphosphate / analogs & derivatives
  • Uridine Triphosphate / metabolism
  • Uridine Triphosphate / pharmacology
  • Viral Proteins / chemistry*
  • Viral Proteins / metabolism
  • Virus Replication / drug effects


  • Antiviral Agents
  • Peptides
  • Uracil Nucleotides
  • VPg protein, poliovirus
  • Viral Proteins
  • Uridine Monophosphate
  • polymerase 3Dpol, poliovirus
  • RNA-Dependent RNA Polymerase
  • Uridine Triphosphate