1KOD

RNA APTAMER COMPLEXED WITH CITRULLINE, NMR

Summary for 1KOD

• Entry DOI: 10.2210/pdb1kod/pdb
• Related: 1KOC
• Descriptor: RNA (5'-R(P*AP*GP*AP*AP*GP*GP*AP*GP*UP*GP*U)-3'), RNA (5'-R(P*AP*CP*GP*GP*UP*UP*AP*GP*GP*UP*CP*GP*CP*U)-3'), CITRULLINE (3 entities in total)
• Functional Keywords: in vitro selected rna, rna aptamer, rna
• Total number of polymer chains: 2
• Total formula weight: 8265.10

Authors

Yang, Y.S.,Kochoyan, M.,Burgstaller, P.,Westhof, E.,Famulok, M. (deposition date: 1996-03-28, release date: 1996-11-08, Last modification date: 2023-11-15)

Primary citation

Yang, Y.,Kochoyan, M.,Burgstaller, P.,Westhof, E.,Famulok, M.
Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy.
Science, 272:1343-1347, 1996

PubMed 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.

PubMed: 8650546

Experimental method

SOLUTION NMR