title: A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA.
abstract: The 5'-terminal cloverleaf (CL)-like RNA structures are essential for the initiation of positive- and negative-strand RNA synthesis of entero- and rhinoviruses. SLD is the cognate RNA ligand of the viral proteinase 3C (3C(pro)), which is an indispensable component of the viral replication initiation complex. The structure of an 18mer RNA representing the apical stem and the cGUUAg D-loop of SLD from the first 5'-CL of BEV1 was determined in solution to a root-mean-square deviation (r.m.s.d.) (all heavy atoms) of 0.59 A (PDB 1Z30). The first (antiG) and last (synA) nucleotide of the D-loop forms a novel 'pseudo base pair' without direct hydrogen bonds. The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1F7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGUUAg BEV D-loop and the cGUAAg tetraloop differ by 1 nt only. Together with the presented binding data, these findings provide independent experimental evidence for our model [O. Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence.
authors.affiliation: Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V. Beutenbergstrasse 11, D-07745 Jena, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Ihle
authors.forename: Oliver
authors.initials: O
authors.lastname: Ohlenschläger
authors.forename: Sabine
authors.initials: S
authors.lastname: Häfner
authors.forename: Elke
authors.initials: E
authors.lastname: Duchardt
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias
authors.forename: Simone
authors.initials: S
authors.lastname: Seitz
authors.forename: Roland
authors.initials: R
authors.lastname: Zell
authors.forename: Ramadurai
authors.initials: R
authors.lastname: Ramachandran
authors.forename: Matthias
authors.initials: M
authors.lastname: Görlach
mesh_terms: D000086042:3C Viral Proteases; D001483:Base Sequence; D003546:Cysteine Endopeptidases / Q000378:metabolism; D029650:Enterovirus, Bovine / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D014764:Viral Proteins / Q000378:metabolism
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins; D003546:Cysteine Endopeptidases; D000086042:3C Viral Proteases