ABSTRACT
The catalysis of reactions involving RNA is similar to the catalysis of analogous reactions on DNA and many catalytic domains of RNA-modification enzymes have close homologs among DNA-modifying enzymes (examples include methyltransferases and deaminases, as exemplified in several other chapters in this book). Crystal structures of RNA modification enzymes have began to unravel how these proteins recognize the correct target nucleoside(s) in large folded or partially folded RNAs. Thus far, three major modes of interaction with the substrate have been found for RNA modification enzymes, distinguished by the character of the structural elements used for specific substrate recognition (Fig. 2). In the first mode, the binding and catalytic func tions are shared by the same domain. In the second mode, catalytic domains are fused to or form a tight complex with specialized RNA-binding domains. In the third mode, the catalytic domain forms a complex with a guide RNA that specifically recognizes the substrate (usually with help of several accessory proteins).
