Recent Progress of Structural Biology of tRNA Processing and Modification

  • Nakanishi, Kotaro (Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology) ;
  • Nureki, Osamu (PRESTO, JST)
  • Received : 2005.04.25
  • Accepted : 2005.04.27
  • Published : 2005.04.30


Transfer RNA (tRNA) is a key molecule to decode the genetic information on mRNA to amino aicds (protein), in a ribosome. For tRNA to fulfill its adopter function, tRNA should be processed into the standard length, and be post-transcriptionally modified. This modification step is essential for the tRNA to maintain the canonical L-shaped structure, which is required for the decoding function of tRNA. Otherwise, it has recently been proposed that modification procedure itself contributes to the RNA (re)folding, where the modification enzymes function as a kind of RNA chaperones. Recent genome analyses and post-genome (proteomics and transcriptomics) analyses have identified genes involved in the tRNA processings and modifications. Furthermore, post-genomic structural analysis has elucidated the structural basis for the tRNA maturation mechanism. In this paper, the recent progress of the structural biology of the tRNA processing and modification is reviewed.


  1. Ishii, R., Minagawa, A., Takaku, H., Takagi, M., Nashimoto, M., et al. (2005) Crystal structure of the tRNA 3′ processing endoribonuclease tRNase Z from Thermotoga maritima. J. Biol. Chem. 280, 14138-14144
  2. Krasilnikov, A. S., Yang, X., Pan, T., and Modragon, A. (2003) Crystal structure of the specificity domain of ribonuclease P. Nature 421, 760-764
  3. Takagi, H., Watanabe, M., Kakuta, Y., Kamachi, R., Numata, T., et al. (2004) Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3. Biochem. Biophys. Res. Commun. 319, 787-794
  4. Tomita, K. and Weiner, A. M. (2001) Collaboration between CC- and A-adding enzymes to build and repair the 3′- terminal CCA of tRNA in Aquifex aeolicus. Science 294, 1334-1336
  5. Tomita, K., Fukai, S., Ishitani, R., Ueda, T., Takeuchi, N., et al. (2004) Structure of a class II CCA-adding enzyme complexed with primer tRNA and an incoming ATP analog. Nature 430, 700-704
  6. Xiong, Y. and Steitz, T. A. (2004) Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 430, 640-645
  7. Hoang, C. and Ferré-D'Amaré, A. R. (2001) Cocrystal structure of a tRNA Y55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell 107, 929-939
  8. Ishii, R., Nureki, O., and Yokoyama, S. (2003) Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus. J. Biol. Chem. 278, 32397-33404
  9. Okabe, M., Tomita, K., Ishitani, R., Ishii, R., Takeuchi, N., et al. (2003) Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. EMBO J. 22, 5918-5927
  10. Ahn, H. J., Kim, H.-W., Yoon, H.-J., Lee, B. I., Suh, S. W., et al. (2003) Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition. EMBO J. 22, 2593-2603
  11. Ishitani, R., Nureki, O., Nameki, N., Okada, N., Nishimura, S., et al. (2003) Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell 113, 383-394
  12. Matsumoto, T., Nishikawa, K., Hori, H., Ohta, T., Miura, K., et al. (1990) Recognition sites of tRNA by a thermostable tRNA (guanosine-2′-)-methyltransferase from Thermus thermophilus HB27. J. Biochem. (Tokyo) 107, 331-338
  13. de la Sierra-Gallay, I. L., Pellegrini, O., and Condon, C. (2005) Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature 433, 657-661
  14. Xie, W., Liu, X., and Huang, R. (2003) Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate. Nat. Struct. Biol. 10, 781-788
  15. Krasilnikov, A. S., Xiao, Y., Pan, T., and Modragón, A. (2004) Basis for structural diversity in homologous RNAs. Science 306, 104-107
  16. Li, F., Xiong, Y., Wang, J., Cho, H. D., Tomita, K., et al. (2002) Crystal structures of the Bacillus stearothermophilus CCAadding enzyme and its complexes with ATP or CTP. Cell 111, 815-824
  17. Numata, T., Ishimatsu, I., Kakuta, Y., Tanaka, I., and Kimura, M. (2004) Crystal structure of archaeal ribonuclease P protein Ph1771P from Pyrococcus Horikoshii Ot3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29. RNA 10, 1423-1432
  18. Nureki, O., Watanabe, K., Fukai, S., Ishii, R., Endo, Y., et al. (2004) Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure 12, 593-602