1z30
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(New page: 200px<br /><applet load="1z30" size="450" color="white" frame="true" align="right" spinBox="true" caption="1z30" /> '''NMR structure of the apical part of stemloop...)
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Revision as of 02:35, 25 November 2007
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NMR structure of the apical part of stemloop D from cloverleaf 1 of bovine enterovirus 1 RNA
Overview
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.
About this Structure
1Z30 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA., Ihle Y, Ohlenschlager O, Hafner S, Duchardt E, Zacharias M, Seitz S, Zell R, Ramachandran R, Gorlach M, Nucleic Acids Res. 2005 Apr 6;33(6):2003-11. Print 2005. PMID:15814817
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