1ddy

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Revision as of 10:33, 8 November 2007

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spinqualitylabelsall models 1ddy, resolution 3.0Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER

Overview

Previous solution structures of ligand-binding RNA aptamers have shown, that molecular recognition is achieved by the folding of an initially, unstructured RNA around its cognate ligand, coupling the processes of RNA, folding and binding. The 3 A crystal structure of the cyanocobalamin, (vitamin B12) aptamer reported here suggests a different approach to, molecular recognition in which elements of RNA secondary structure combine, to create a solvent-accessible docking surface for a large, complex, ligand. Central to this structure is a locally folding RNA triplex, stabilized by a novel three-stranded zipper. Perpendicular stacking of a, duplex on this triplex creates a cleft that functions as the vitamin B12, binding site. Complementary packing of hydrophobic surfaces, direct, hydrogen bonding and dipolar interactions between the ligand and the RNA, appear to contribute to binding. The nature of the interactions that, stabilize complex formation and the possible uncoupling of folding and, binding for this RNA suggest a strong mechanistic similarity to typical, protein-ligand complexes.

About this Structure

1DDY is a Protein complex structure of sequences from [1] with B12 and NME as ligands. Full crystallographic information is available from OCA.

Reference

The structural basis for molecular recognition by the vitamin B 12 RNA aptamer., Sussman D, Nix JC, Wilson C, Nat Struct Biol. 2000 Jan;7(1):53-7. PMID:10625428

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