Structural aspects of translation termination on the ribosome

RNA

Volumn 17, Issue 8, 2011, Pages 1409-1421

  Korostelev, Andrei A ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

70S ribosome; Crystal structures; Release factors; RF1; RF2

Indexed keywords

AMINO ACID; GUANOSINE TRIPHOSPHATASE; MESSENGER RNA; PEPTIDYL CARRIER PROTEIN; POLYPEPTIDE; RIBOSOME RNA; TRANSFER RNA; TRANSLATION TERMINATION FACTOR;

BIOCHEMISTRY; CATALYSIS; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; HUMAN; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN HYDROLYSIS; PROTEIN SECRETION; PROTEIN SYNTHESIS; REVIEW; RIBOSOME; RNA TRANSLATION; STOP CODON; THERMUS THERMOPHILUS;

ANIMALS; CODON, TERMINATOR; HUMANS; HYDROLYSIS; PEPTIDE TERMINATION FACTORS; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, TRANSFER, AMINO ACYL;

BACTERIA (MICROORGANISMS);

EID: 79960471842     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2733411     Document Type: Review

References (121)

1. Alkalaeva EZ, Pisarev AV, Frolova LY, Kisselev LL, Pestova TV. 2006. In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell 125: 1125-1136.
2. Arkov AL, Murgola EJ. 1999. Ribosomal RNAs in translation termination: Facts and hypotheses. Biochemistry (Mosc) 64: 1354-1359. (Pubitemid 129597019)
3. Baierlein C, Krebber H. 2010. Translation termination: New factors and insights. RNA Biol 7: 548-550.
4. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289: 905-920. (Pubitemid 30659939)
5. Barthelme D, Dinkelaker S, Albers SV, Londei P, Ermler U, Tampe R. 2011. Ribosome recycling depends on a mechanistic link between the FeS cluster domain and a conformational switch of the twin-ATPase ABCE1. Proc Natl Acad Sci 108: 3228-3233.
6. Ben-Shem A, Jenner L, Yusupova G, Yusupov M. 2010. Crystal structure of the eukaryotic ribosome. Science 330: 1203-1209.
7. Bertram G, Bell HA, Ritchie DW, Fullerton G, Stansfield I. 2000. Terminating eukaryote translation: Domain 1 of release factor eRF1 functions in stop codon recognition. RNA 6: 1236-1247.
8. Bokov K, Steinberg SV. 2009. A hierarchical model for evolution of 23S ribosomal RNA. Nature 457: 977-980.
9. Bouakaz L, Bouakaz E, Murgola EJ, Ehrenberg M, Sanyal S. 2006. The role of ribosomal protein L11 in class I release factor-mediated translation termination and translational accuracy. J Biol Chem 281: 4548-4556. (Pubitemid 43847887)
10. Brenner S, Stretton AO, Kaplan S. 1965. Genetic code: The "nonsense" triplets for chain termination and their suppression. Nature 206: 994-998.
11. Brenner S, Barnett L, Katz ER, Crick FH. 1967. UGA: A third nonsense triplet in the genetic code. Nature 213: 449-450.
12. Brown CM, Tate WP. 1994. Direct recognition of mRNA stop signals by Escherichia coli polypeptide chain release factor two. J Biol Chem 269: 33164-33170.
13. Brunelle JL, Shaw JJ, Youngman EM, Green R. 2008. Peptide release on the ribosome depends critically on the 2′-OH of the peptidyl-tRNA substrate. RNA 14: 1526-1531.
14. Buckingham RH, Grentzmann G, Kisselev L. 1997. Polypeptide chain release factors. Mol Microbiol 24: 449-456. (Pubitemid 27241693)
15. Capecchi MR. 1967. Polypeptide chain termination in vitro: Isolation of a release factor. Proc Natl Acad Sci 58: 1144-1151.
16. Caskey CT. 1980. Peptide chain termination. Trends Biochem Sci 5: 234-237.
17. Caskey CT, Beaudet AL, Scolnick EM, Rosman M. 1971. Hydrolysis of fMet-tRNA by peptidyl transferase. Proc Natl Acad Sci 68: 3163-3167.
18. Czaplinski K, Ruiz-Echevarria MJ, Paushkin SV, Han X, Weng Y, Perlick HA, Dietz HC, Ter-Avanesyan MD, Peltz SW. 1998. The surveillance complex interacts with the translation release factors to enhance termination and degrade aberrant mRNAs. Genes Dev 12: 1665-1677. (Pubitemid 28299517)
19. Dalgarno L, Shine J. 1973. Conserved terminal sequence in 18SrRNA may represent terminator anticodons. Nat New Biol 245: 261-262.
20. DeLano WL. 2002. The PyMOL molecular graphics system. DeLano Scientific, Palo Alto, CA.
21. Dincbas-Renqvist V, Engstrom A, Mora L, Heurgue-Hamard V, Buckingham R, Ehrenberg M. 2000. A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation. EMBO J 19: 6900-6907. (Pubitemid 32011683)
22. Dontsova M, Frolova L, Vassilieva J, Piendl W, Kisselev L, Garber M. 2000. Translation termination factor aRF1 from the archaeon Methanococcus jannaschii is active with eukaryotic ribosomes. FEBS Lett 472: 213-216. (Pubitemid 30224466)
23. Dorner S, Polacek N, Schulmeister U, Panuschka C, Barta A. 2002. Molecular aspects of the ribosomal peptidyl transferase. Biochem Soc Trans 30: 1131-1136.
24. Dorner S, Panuschka C, Schmid W, Barta A. 2003. Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2′-OH to activity. Nucleic Acids Res 31: 6536-6542. (Pubitemid 37508758)
25. Felder CE, Prilusky J, Silman I, Sussman JL. 2007. A server and database for dipole moments of proteins. Nucleic Acids Res 35: W512-W521.
26. Freistroffer DV, Pavlov MY, MacDougall J, Buckingham RH, Ehrenberg M. 1997. 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 16: 4126-4133. (Pubitemid 27281027)
27. Freistroffer DV, Kwiatkowski M, Buckingham RH, Ehrenberg M. 2000. The accuracy of codon recognition by polypeptide release factors. Proc Natl Acad Sci 97: 2046-2051. (Pubitemid 30134019)
28. Frolova L, Le Goff X, Rasmussen HH, Cheperegin S, Drugeon G, Kress M, Arman I, Haenni AL, Celis JE, Philippe M, et al. 1994. A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor. Nature 372: 701-703.
29. Frolova L, Le Goff X, Zhouravleva G, Davydova E, Philippe M, Kisselev L. 1996. Eukaryotic polypeptide chain release factor eRF3 is an eRF1- and ribosome-dependent guanosine triphosphatase. RNA 2: 334-341. (Pubitemid 26371285)
30. Frolova LY, Tsivkovskii RY, Sivolobova GF, Oparina NY, Serpinsky OI, Blinov VM, Tatkov SI, Kisselev LL. 1999. Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis. RNA 5: 1014-1020. (Pubitemid 29365331)
31. Frolova L, Seit-Nebi A, Kisselev L. 2002. Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1. RNA 8: 129-136. (Pubitemid 34288901)
32. Grentzmann G, Brechemier-Baey D, Heurgue V, Mora L, Buckingham RH. 1994. Localization and characterization of the gene encoding release factor RF3 in Escherichia coli. Proc Natl Acad Sci 91: 5848-5852. (Pubitemid 24188239)
33. Gromadski KB, Rodnina MV. 2004. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol Cell 13: 191-200. (Pubitemid 38183266)
34. Gutell RR, Weiser B, Woese CR, Noller HF. 1985. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol 32: 155-216.
35. He SL, Green R. 2010. Visualization of codon-dependent conformational rearrangements during translation termination. Nat Struct Mol Biol 17: 465-470.
36. Hetrick B, Lee K, Joseph S. 2009. Kinetics of stop codon recognition by release factor 1. Biochemistry 48: 11178-11184.
37. Hoshino S, Imai M, Kobayashi T, Uchida N, Katada T. 1999. The eukaryotic polypeptide chain releasing factor (eRF3/GSPT) carrying the translation termination signal to the 3′-Poly(A) tail of mRNA. Direct association of erf3/GSPT with polyadenylate-binding protein. J Biol Chem 274: 16677-16680.
38. Ito K, Ebihara K, Uno M, Nakamura Y. 1996. Conserved motifs in prokaryotic and eukaryotic polypeptide release factors: tRNA-protein mimicry hypothesis. Proc Natl Acad Sci 93: 5443-5448. (Pubitemid 26159469)
39. Ito K, Uno M, Nakamura Y. 1998. Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons. Proc Natl Acad Sci 95: 8165-8169. (Pubitemid 28326084)
40. Ito K, Uno M, Nakamura Y. 2000. A tripeptide "anticodon" deciphers stop codons in messenger RNA. Nature 403: 680-684.
41. Ivanov V, Beniaminov A, Mikheyev A, Minyat E. 2001. A mechanism for stop codon recognition by the ribosome: A bioinformatic approach. RNA 7: 1683-1692. (Pubitemid 34042283)
42. Jaeger KE, Dijkstra BW, Reetz MT. 1999. Bacterial biocatalysts: Molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu Rev Microbiol 53: 315-351. (Pubitemid 29503734)
43. Jenner LB, Demeshkina N, Yusupova G, Yusupov M. 2010. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat Struct Mol Biol 17: 555-560.
44. Jin H, Kelley AC, Loakes D, Ramakrishnan V. 2010. Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release. Proc Natl Acad Sci 107: 8593-8598.
45. Jorgensen F, Adamski FM, Tate WP, Kurland CG. 1993. Release factor-dependent false stops are infrequent in Escherichia coli. J Mol Biol 230: 41-50. (Pubitemid 23093546)
46. Khoshnevis S, Gross T, Rotte C, Baierlein C, Ficner R, Krebber H. 2010. The iron-sulphur protein RNase L inhibitor functions in translation termination. EMBO Rep 11: 214-219.
47. Klaholz BP, Pape T, Zavialov AV, Myasnikov AG, Orlova EV, Vestergaard B, Ehrenberg M, van Heel M. 2003. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421: 90-94. (Pubitemid 36077091)
48. Klein DJ, Moore PB, Steitz TA. 2004. The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J Mol Biol 340: 141-177. (Pubitemid 38739442)
49. Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, Zhu J, Trakhanov S, Scott WG, Noller HF. 2008. Crystal structure of a translation termination complex formed with release factor RF2. Proc Natl Acad Sci 105: 19684-19689.
50. Korostelev A, Zhu J, Asahara H, Noller HF. 2010. Recognition of the amber UAG stop codon by release factor RF1. EMBO J 29: 2577-2585.
51. Kushnirov VV, Ter-Avanesyan MD, Telckov MV, Surguchov AP, Smirnov VN, Inge-Vechtomov SG. 1988. Nucleotide sequence of the SUP2 (SUP35) gene of Saccharomyces cerevisiae. Gene 66: 45-54.
52. Laurberg M, Asahara H, Korostelev A, Zhu J, Trakhanov S, Noller HF. 2008. Structural basis for translation termination on the 70S ribosome. Nature 454: 852-857.
53. Le Roy F, Salehzada T, Bisbal C, Dougherty JP, Peltz SW. 2005. A newly discovered function for RNase L in regulating translation termination. Nat Struct Mol Biol 12: 505-512. (Pubitemid 43085880)
54. Ma B, Nussinov R. 2004. Release factors eRF1 and RF2: A universal mechanism controls the large conformational changes. J Biol Chem 279: 53875-53885. (Pubitemid 40051897)
55. Maegley KA, Admiraal SJ, Herschlag D. 1996. Ras-catalyzed hydrolysis of GTP: A new perspective from model studies. Proc Natl Acad Sci 93: 8160-8166. (Pubitemid 26269527)
56. Maquat LE. 2004. Nonsense-mediated mRNA decay: Splicing, translation, and mRNP dynamics. Nat Rev Mol Cell Biol 5: 89-99. (Pubitemid 38160252)
57. Mikuni O, Ito K, Moffat J, Matsumura K, McCaughan K, Nobukuni T, Tate W, Nakamura Y. 1994. Identification of the prfC gene, which encodes peptide-chain-release factor 3 of Escherichia coli. Proc Natl Acad Sci 91: 5798-5802. (Pubitemid 24188229)
58. Mitkevich VA, Kononenko AV, Petrushanko IY, Yanvarev DV, Makarov AA, Kisselev LL. 2006. Termination of translation in eukaryotes is mediated by the quaternary eRF1*eRF3*GTP*Mg2+ complex. The biological roles of eRF3 and prokaryotic RF3 are profoundly distinct. Nucleic Acids Res 34: 3947-3954.
59. Mora L, Heurgue-Hamard V, Champ S, Ehrenberg M, Kisselev LL, Buckingham RH. 2003. The essential role of the invariant GGQ motif in the function and stability in vivo of bacterial release factors RF1 and RF2. Mol Microbiol 47: 267-275. (Pubitemid 36051340)
60. Mora L, Heurgue-Hamard V, de Zamaroczy M, Kervestin S, Buckingham RH. 2007. Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo. J Biol Chem 282: 35638-35645. (Pubitemid 350277100)
61. Nakamura Y, Ito K, Matsumura K, Kawazu Y, Ebihara K. 1995. Regulation of translation termination: Conserved structural motifs in bacterial and eukaryotic polypeptide release factors. Biochem Cell Biol 73: 1113-1122.
62. Neu-Yilik G, Kulozik AE. 2008. NMD: Multitasking between mRNA surveillance and modulation of gene expression. Adv Genet 62: 185-243.
63. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J. 1995. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270: 1464-1472.
64. Noller HF. 1999. On the origin of the ribosome: Coevolution of subdomains of tRNA and rRNA. In The RNA world, 2nd ed. (ed. R Gesteland et al.), pp. 197-219. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
65. Noller HF. 2004. The driving force for molecular evolution of translation. RNA 10: 1833-1837. (Pubitemid 39557819)
66. Noller HF. 2006. Evolution of ribosomes and translation from an RNA world. In The RNA world, 3rd ed. (ed. R Gesteland et al.), pp. 287-307. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
67. Noller HF. 2010. Evolution of protein synthesis from an RNA World. Cold Spring Harb Perspect Biol a003681. doi: 10.1101/cshperspect.a003681.
68. Noller HF, Woese CR. 1981. Secondary structure of 16S ribosomal RNA. Science 212: 403-411. (Pubitemid 11041929)
69. Nozaki Y, Matsunaga N, Ishizawa T, Ueda T, Takeuchi N. 2008. HMRF1L is a human mitochondrial translation release factor involved in the decoding of the termination codons UAA and UAG. Genes Cells 13: 429-438. (Pubitemid 351567045)
70. Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V. 2001. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292: 897-902.
71. Orlova M, Yueh A, Leung J, Goff SP. 2003. Reverse transcriptase of Moloney murine leukemia virus binds to eukaryotic release factor 1 to modulate suppression of translational termination. Cell 115: 319-331. (Pubitemid 37487705)
72. Pape T, Wintermeyer W, Rodnina M. 1999. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J 18: 3800-3807. (Pubitemid 29308859)
73. Petry S, Brodersen DE, Murphy FV IV, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V. 2005. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell 123: 1255-1266.
74. Pisarev AV, Skabkin MA, Pisareva VP, Skabkina OV, Rakotondrafara AM, Hentze MW, Hellen CU, Pestova TV. 2010. The role of ABCE1 in eukaryotic post-termination ribosomal recycling. Mol Cell 37: 196-210.
75. Rawat UBS, Zavialov AV, Sengupta J, Valle M, Grassucci RA, Linde J, Vestergaard B, Ehrenberg M, Frank J. 2003. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421: 87-90. (Pubitemid 36077090)
76. Rawat U, Gao H, Zavialov A, Gursky R, Ehrenberg M, Frank J. 2006. Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM. J Mol Biol 357: 1144-1153. (Pubitemid 43357978)
77. Rodnina MV, Pape T, Fricke R, Kuhn L, Wintermeyer W. 1996. Initial binding of the elongation factor Tu.GTP.aminoacyl-tRNA complex preceding codon recognition on the ribosome. J Biol Chem 271: 646-652.
78. Rodnina MV, Beringer M, Wintermeyer W. 2006. Mechanism of peptide bond formation on the ribosome. Q Rev Biophys 39: 203-225. (Pubitemid 44950378)
79. Salas-Marco J, Bedwell DM. 2004. GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination. Mol Cell Biol 24: 7769-7778. (Pubitemid 39121500)
80. Sato H, Ito K, Nakamura Y. 2006. Ribosomal protein L11 mutations in two functional domains equally affect release factors 1 and 2 activity. Mol Microbiol 60: 108-120. (Pubitemid 43363291)
81. Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA. 2005a. Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol Cell 20: 437-448. (Pubitemid 41572300)
82. Schmeing TM, Huang KS, Strobel SA, Steitz TA. 2005b. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438: 520-524. (Pubitemid 41742026)
83. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. 2005. Structures of the bacterial ribosome at 3.5 A resolution. Science 310: 827-834. (Pubitemid 41567336)
84. Seit Nebi A, Frolova L, Ivanova N, Poltaraus A, Kiselev L. 2000. Mutation of a glutamine residue in the universal tripeptide GGQ in human eRF1 termination factor does not cause complete loss of its activity. Mol Biol (Mosk) 34: 899-900.
85. Seit-Nebi A, Frolova L, Justesen J, Kisselev L. 2001. Class-1 translation termination factors: Invariant GGQ minidomain is essential for release activity and ribosome binding but not for stop codon recognition. Nucleic Acids Res 29: 3982-3987. (Pubitemid 32962688)
86. Selmer M, Dunham CM, Murphy FV, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V. 2006. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313: 1935-1942.
87. Shaw JJ, Green R. 2007. Two distinct components of release factor function uncovered by nucleophile partitioning analysis. Mol Cell 28: 458-467. (Pubitemid 350030565)
88. Shin DH, Brandsen J, Jancarik J, Yokota H, Kim R, Kim SH. 2004. Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome. J Mol Biol 341: 227-239. (Pubitemid 39090647)
89. Shine J, Dalgarno L. 1974. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci 71: 1342-1346.
90. Simonović M, Steitz TA. 2008. Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3′-hydroxyl group of A76 of the unacylated A-site tRNA. RNA 14: 2372-2378.
91. Soleimanpour-Lichaei HR, Kuhl I, Gaisne M, Passos JF, Wydro M, Rorbach J, Temperley R, Bonnefoy N, Tate W, Lightowlers R, et al. 2007. mtRF1a is a human mitochondrial translation release factor decoding the major termination codons UAA and UAG. Mol Cell 27: 745-757. (Pubitemid 47333220)
92. Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D. 2000. The crystal structure of human eukaryotic release factor eRF1-mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Cell 100: 311-321. (Pubitemid 30353087)
93. Stansfield I, Jones KM, Kushnirov VV, Dagkesamanskaya AR, Poznyakovski AI, Paushkin SV, Nierras CR, Cox BS, Ter-Avanesyan MD, Tuite MF. 1995. The products of the SUP45 (eRF1) and SUP35 genes interact to mediate translation termination in Saccharomyces cerevisiae. EMBO J 14: 4365-4373.
94. Sund J, Ander M, Aqvist J. 2010. Principles of stop-codon reading on the ribosome. Nature 465: 947-950.
95. Tate W, Greuer B, Brimacombe R. 1990. Codon recognition in polypeptide chain termination: Site directed crosslinking of termination codon to Escherichia coli release factor 2. Nucleic Acids Res 18: 6537-6544.
96. Temperley R, Richter R, Dennerlein S, Lightowlers RN, Chrzanowska- Lightowlers ZM. 2010. Hungry codons promote frameshifting in human mitochondrial ribosomes. Science 327: 301. doi: 10.1126/science.1180674.
97. Thompson RC. 1988. EFTu provides an internal kinetic standard for translational accuracy. Trends Biochem Sci 13: 91-93.
98. Tompkins RK, Scolnick EM, Caskey CT. 1970. Peptide chain termination. VII. The ribosomal and release factor requirements for peptide release. Proc Natl Acad Sci 65: 702-708.
99. Trobro S, Aqvist J. 2007. A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis. Mol Cell 27: 758-766. (Pubitemid 47333221)
100. Trobro S, Aqvist J. 2009. Mechanism of the translation termination reaction on the ribosome. Biochemistry 48: 11296-11303.
101. Vestergaard B, Van LB, Andersen GR, Nyborg J, Buckingham RH, Kjeldgaard M. 2001. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol Cell 8: 1375-1382. (Pubitemid 34085006)
102. Vestergaard B, Sanyal S, Roessle M, Mora L, Buckingham RH, Kastrup JS, Gajhede M, Svergun DI, Ehrenberg M. 2005. The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure. Mol Cell 20: 929-938. (Pubitemid 41814881)
103. Vogel Z, Zamir A, Elson D. 1969. The possible involvement of peptidyl transferase in the termination step of protein biosynthesis. Biochemistry 8: 5161-5168.
104. Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V. 2009. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 16: 528-533.
105. Wang W, Czaplinski K, Rao Y, Peltz SW. 2001. The role of Upf proteins in modulating the translation read-through of nonsense-containing transcripts. EMBO J 20: 880-890. (Pubitemid 32167652)
106. Weinger JS, Parnell KM, Dorner S, Green R, Strobel SA. 2004. Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat Struct Mol Biol 11: 1101-1106. (Pubitemid 39453339)
107. Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, Kelley AC, Ramakrishnan V. 2008. Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322: 953-956.
108. Wilmouth RC, Edman K, Neutze R, Wright PA, Clifton IJ, Schneider TR, Schofield CJ, Hajdu J. 2001. X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate. Nat Struct Biol 8: 689-694. (Pubitemid 32757928)
109. Wilson PG, Culbertson MR. 1988. SUF12 suppressor protein of yeast. A fusion protein related to the EF-1 family of elongation factors. J Mol Biol 199: 559-573.
110. Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. 2000. Structure of the 30S ribosomal subunit. Nature 407: 327-339.
111. Woese CR, Fox GE, Zablen L, Uchida T, Bonen L, Pechman K, Lewis BJ, Stahl D. 1975. Conservation of primary structure in 16S ribosomal RNA. Nature 254: 83-86.
112. Wohlgemuth I, Pohl C, Rodnina MV. 2010. Optimization of speed and accuracy of decoding in translation. EMBO J 29: 3701-3709.
113. Young DJ, Edgar CD, Murphy J, Fredebohm J, Poole ES, Tate WP. 2010a. Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria. RNA 16: 1146-1155.
114. Young DJ, Edgar CD, Poole ES, Tate WP. 2010b. The codon specificity of eubacterial release factors is determined by the sequence and size of the recognition loop. RNA 16: 1623-1633.
115. Youngman EM, He SL, Nikstad LJ, Green R. 2007. Stop codon recognition by release factors induces structural rearrangement of the ribosomal decoding center that is productive for peptide release. Mol Cell 28: 533-543. (Pubitemid 350137792)
116. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF. 2001. Crystal structure of the ribosome at 5.5 A resolution. Science 292: 883-896. (Pubitemid 32422479)
117. Zaher HS, Shaw JJ, Strobel SA, Green R. 2011. The 2′-OH group of the peptidyl-tRNA stabilizes an active conformation of the ribosomal PTC. EMBO J doi: 10.1038/emboj.2011.142.
118. Zavialov AV, Buckingham RH, Ehrenberg M. 2001. A post-termination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107: 115-124. (Pubitemid 32972042)
119. Zavialov AV, Mora L, Buckingham RH, Ehrenberg M. 2002. Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3. Mol Cell 10: 789-798. (Pubitemid 35335634)
120. Zhouravleva G, Frolova L, Le Goff X, Le Guellec R, Inge-Vechtomov S, Kisselev L, Philippe M. 1995. Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and eRF3. EMBO J 14: 4065-4072.
121. Zoldak G, Redecke L, Svergun DI, Konarev PV, Voertler CS, Dobbek H, Sedlak E, Sprinzl M. 2007. Release factors 2 from Escherichia coli and Thermus thermophilus: Structural, spectroscopic, and microcalorimetric studies. Nucleic Acids Res 35: 1343-1353. (Pubitemid 46522984)