Isoleucine:RNA sites with associated coding sequences.
An RNA family that binds isoleucine with Kd = 200-500 microM was repetitively isolated from a ribonucleotide transcript pool containing 50 randomized positions. The RNA site is specific, discriminating against branched side chains of different size (valine--one methylene smaller than isoleucine) by at least 1.3 kcal/mol and against the shape (linear) of norleucine by 0.6 kcal/mol. The binding site was localized by sequence comparison, by synthesis of mutant and truncated active derivatives, and by chemical modification-interference. The binding site is small, no more than 10-12 nt, containing an asymmetric internal loop (6 over 2 nt) that includes the isoleucine codon AUU and a sequence of four G's, two of which are involved in G-U and G-C base pairs. Areas of U/G concentration like these may signal a hydrophobic RNA site.
Majerfeld
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I
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347, USA.
Yarus
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M
D000577:Amides / Q000378:metabolism; D000596:Amino Acids / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D002846:Chromatography, Affinity; D007532:Isoleucine / Q000378:metabolism*; D007854:Lead / Q000494:pharmacology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D015032:Zinc / Q000378:metabolism
D000577:Amides; D000596:Amino Acids; D007532:Isoleucine; D007854:Lead; D012313:RNA; D015032:Zinc