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We describe here analyses of the secondary structure of ATP-binding ribonucleopeptide (RNP) receptors. Mapping of the RNA structure of ATP-binding RNP receptors by using hydrolytic enzymes, chemical probing with dimethyl sulfate (DMS), and in-line probing indicated that ATP-binding RNP receptors take the loop structure at the nucleotide position of the "variable region". In addition, it was evident that a part of the consensus region located next to the variable region directly participated in the binding to ATP. The completely preserved three U nucleotides were essential for the binding of RNP to ATP as revealed by the affinity evaluation and the secondary structure analyses of the U nucleotides mutants of the ATP-binding RNP receptor. Interestingly, two mutants with an adenosine introduced to either of the two U nucleotides showed similar secondary structures to the original ATP-binding RNP. These results imply the possibility that the adenine base introduced at the U position acts just like the substrate ATP, and suggest that the U nucleotides in these positions interact directly to ATP.

Structural aspects for the function of ATP-binding ribonucleopeptide receptors