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. 2001 Jan;7(1):64–70. doi: 10.1017/s1355838201001704

Functional mapping of ribosome-contact sites in the ribosome recycling factor: a structural view from a tRNA mimic.

T Fujiwara 1, K Ito 1, Y Nakamura 1
PMCID: PMC1370070  PMID: 11214182

Abstract

Ribosome recycling factor (RRF) is required for disassembly of the posttermination complex of the ribosome after release of polypeptides. The crystal structure of RRF resembles a tRNA shape, with an architecturally different flexibility compared with tRNA, but its structure-and-function relationships are unknown. We here found that an RRF variant defective in ribosome binding regains the binding capacity through 20 independent secondary changes occurring in three topologically distinct regions of RRF. Because two of these regions are equivalent to the tip of the anticodon stem and the upper surface of the acceptor stem of tRNA, RRF may interact with the ribosome in a way similar to tRNA, spanning 30S and 50S subunits, to exert its action for splitting the ribosome.

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Selected References

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  1. Beckman R. A., Mildvan A. S., Loeb L. A. On the fidelity of DNA replication: manganese mutagenesis in vitro. Biochemistry. 1985 Oct 8;24(21):5810–5817. doi: 10.1021/bi00342a019. [DOI] [PubMed] [Google Scholar]
  2. Cammack K. A., Wade H. E. The sedimentation behaviour of ribonuclease-active and -inactive ribosomes from bacteria. Biochem J. 1965 Sep;96(3):671–680. doi: 10.1042/bj0960671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cate J. H., Yusupov M. M., Yusupova G. Z., Earnest T. N., Noller H. F. X-ray crystal structures of 70S ribosome functional complexes. Science. 1999 Sep 24;285(5436):2095–2104. doi: 10.1126/science.285.5436.2095. [DOI] [PubMed] [Google Scholar]
  4. Celano B., Pawlik R. T., Gualerzi C. O. Interaction of Escherichia coli translation-initiation factor IF-1 with ribosomes. Eur J Biochem. 1988 Dec 15;178(2):351–355. doi: 10.1111/j.1432-1033.1988.tb14457.x. [DOI] [PubMed] [Google Scholar]
  5. Freistroffer D. V., Pavlov M. Y., MacDougall J., Buckingham R. H., Ehrenberg M. Release factor RF3 in E.coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner. EMBO J. 1997 Jul 1;16(13):4126–4133. doi: 10.1093/emboj/16.13.4126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fujiwara T., Ito K., Nakayashiki T., Nakamura Y. Amber mutations in ribosome recycling factors of Escherichia coli and Thermus thermophilus: evidence for C-terminal modulator element. FEBS Lett. 1999 Mar 26;447(2-3):297–302. doi: 10.1016/s0014-5793(99)00302-6. [DOI] [PubMed] [Google Scholar]
  7. Hirashima A., Kaji A. Factor-dependent release of ribosomes from messenger RNA. Requirement for two heat-stable factors. J Mol Biol. 1972 Mar 14;65(1):43–58. doi: 10.1016/0022-2836(72)90490-1. [DOI] [PubMed] [Google Scholar]
  8. Ito K., Uno M., Nakamura Y. A tripeptide 'anticodon' deciphers stop codons in messenger RNA. Nature. 2000 Feb 10;403(6770):680–684. doi: 10.1038/35001115. [DOI] [PubMed] [Google Scholar]
  9. Janosi L., Hara H., Zhang S., Kaji A. Ribosome recycling by ribosome recycling factor (RRF)--an important but overlooked step of protein biosynthesis. Adv Biophys. 1996;32:121–201. doi: 10.1016/0065-227x(96)84743-5. [DOI] [PubMed] [Google Scholar]
  10. Janosi L., Mottagui-Tabar S., Isaksson L. A., Sekine Y., Ohtsubo E., Zhang S., Goon S., Nelken S., Shuda M., Kaji A. Evidence for in vivo ribosome recycling, the fourth step in protein biosynthesis. EMBO J. 1998 Feb 16;17(4):1141–1151. doi: 10.1093/emboj/17.4.1141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Karimi R., Pavlov M. Y., Buckingham R. H., Ehrenberg M. Novel roles for classical factors at the interface between translation termination and initiation. Mol Cell. 1999 May;3(5):601–609. doi: 10.1016/s1097-2765(00)80353-6. [DOI] [PubMed] [Google Scholar]
  12. Kim K. K., Min K., Suh S. W. Crystal structure of the ribosome recycling factor from Escherichia coli. EMBO J. 2000 May 15;19(10):2362–2370. doi: 10.1093/emboj/19.10.2362. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Oshima T., Ito K., Kabayama H., Nakamura Y. Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp. Mol Gen Genet. 1995 Jun 10;247(5):521–528. doi: 10.1007/BF00290342. [DOI] [PubMed] [Google Scholar]
  14. Pavlov M. Y., Freistroffer D. V., MacDougall J., Buckingham R. H., Ehrenberg M. Fast recycling of Escherichia coli ribosomes requires both ribosome recycling factor (RRF) and release factor RF3. EMBO J. 1997 Jul 1;16(13):4134–4141. doi: 10.1093/emboj/16.13.4134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Pestka S. Studies on the formation of transfer ribonucleic acid-ribosome complexes. 3. The formation of peptide bonds by ribosomes in the absence of supernatant enzymes. J Biol Chem. 1968 May 25;243(10):2810–2820. [PubMed] [Google Scholar]
  16. Selmer M., Al-Karadaghi S., Hirokawa G., Kaji A., Liljas A. Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic. Science. 1999 Dec 17;286(5448):2349–2352. doi: 10.1126/science.286.5448.2349. [DOI] [PubMed] [Google Scholar]
  17. Toyoda T., Tin O. F., Ito K., Fujiwara T., Kumasaka T., Yamamoto M., Garber M. B., Nakamura Y. Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch. RNA. 2000 Oct;6(10):1432–1444. doi: 10.1017/s1355838200001060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Uno M., Ito K., Nakamura Y. Functional specificity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor 2. Biochimie. 1996;78(11-12):935–943. doi: 10.1016/s0300-9084(97)86715-6. [DOI] [PubMed] [Google Scholar]
  19. Yoshizawa S., Fourmy D., Puglisi J. D. Recognition of the codon-anticodon helix by ribosomal RNA. Science. 1999 Sep 10;285(5434):1722–1725. doi: 10.1126/science.285.5434.1722. [DOI] [PubMed] [Google Scholar]

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