1i4c

From Proteopedia

proteopedia linkproteopedia link

spinqualitylabelsall models 1i4c Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

THE SOLUTION STRUCTURE OF THE MINOR FAMILY OF THE MUTANT STEM LOOP C 5'UUA3' TRILOOP OF BROME MOSAIC VIRUS (+) STRAND RNA

Overview

The 3'-end region of the genomic RNA of brome mosaic virus forms a, tRNA-like structure that is critical for its replication. Previous studies, have shown that in this region, a stem-loop structure, called SLC, is, necessary and sufficient for the binding of the RNA replicase, and for RNA, replication. Recently, we determined the high-resolution NMR structure of, SLC, which demonstrated that a 5'-AUA-3' triloop region is an important, structural element for the enzymatic recognition. We proposed that the, 5'-adenine of the triloop, which is rigidly fixed ("clamped") to the stem, is a key recognition element for the replicase. To elucidate the role of, this "clamped base motif" for the enzymatic recognition, we have now, investigated the solution conformations of several stem-loop molecules, with mutant triloops, 5'-UUA-3', 5'-GUA-3', 5'-CUA-3' and 5'-UUU-3', that, destroy the enzymatic recognition. For the GUA and UUA mutants, we have, obtained high-resolution solution structures using 2D NMR. All four, mutants have very similar thermodynamic stabilities, and all have the same, secondary structures, a triloop with a five base-paired stem helix. In, addition, they have quite similar sugar puckering patterns in the triloop, region. The NMR structures of the GUA and UUA show that the 5' nucleotide, of the triloop (G6 in GUA or U6 in UUA) lacks the strong interactions that, hold its base in a fixed position. In particular, the U6 of UUA is found, in two different conformations. Neither of these two mutants has the, clamped base motif that was observed in the wild-type. While UUA also, shows global change in the overall triloop conformation, GUA shows a very, similar triloop conformation to the wild-type except for the lack of this, motif. The absence of the clamped base motif is the only common structural, difference between these two mutants and the wild-type. These results, clearly indicate that the loss of function of the UUA and GUA mutants, comes mainly from the destruction of a small key recognition motif rather, than from global changes in their triloop conformations. Based on this, study, we conclude that the key structural motif in the triloop recognized, by the replicase is a solution-exposed, 5'-adenine base in the triloop, that is clamped to the stem helix, which is called a clamped adenine, motif.

About this Structure

1I4C is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoter., Kim CH, Tinoco I Jr, J Mol Biol. 2001 Mar 30;307(3):827-39. PMID:11273704

Page seeded by OCA on Sun Nov 25 03:36:26 2007