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Structure, dynamics, and function of RNA modification enzymes

Ryuichiro Ishitani1, Shigeyuki Yokoyama2 and Osamu Nureki1

1Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan

2Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

Available online 5 June 2008. 

Most noncoding RNAs (ncRNAs) are post-transcriptionally modified, which generally reinforces the specific tertiary structure of the RNAs to accelerate their functions. Biochemical and structural investigations of RNA modification have primarily focused on ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), the best-characterized ncRNAs, which play central roles in the translation of the genetic code. Especially in tRNA, modifications not only stabilize the L-shaped tertiary structure but also alter its function by improving and switching its molecular recognition. Furthermore, it has recently been proposed that the modification procedure itself contributes to the RNA (re)folding, in which the modification enzymes function as RNA chaperones. Recent genome and postgenome (proteomics and transcriptomics) analyses have identified new genes encoding enzymes responsible for ncRNA modifications. Further structural analyses of RNA-modification enzyme complexes have elucidated the structural basis by which the modification enzymes specifically recognize the target RNAs and ingeniously incorporate the chemical modifications into the precise position. This paper provides an overview of the recent progress in the structural biology of ncRNA-modification enzymes.