PMID: 8650546 , Related PDB ids: 1KOC, 1KOD

Authors:

Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M

Title:

Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy.

Journal:

Science. 1996 May 31;272(5266):1343-7.

Abstract:

In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.