The mechanism of peptidyl transfer catalysis by the ribosome

Annual Review of Biochemistry

Volumn 80, Issue , 2011, Pages 527-555

  Leung, Edward Ki Yun ^a   Suslov, Nikolai ^a   Tuttle, Nicole ^a   Sengupta, Raghuvir ^b   Piccirilli, Joseph Anthony ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

entropy trap; induced fit; peptide bond formation; peptidyl transferase center; translation

Indexed keywords

AMIDE; AMINOACYL TRANSFER RNA; HYDROGEN; NITROGEN; NUCLEOPHILE; PEPTIDYLTRANSFERASE; RNA 23S; TRANSFER RNA; WATER;

ARTICLE; BIOCATALYSIS; COMPUTER MODEL; CRYSTAL STRUCTURE; ENTHALPY; ENTROPY; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; HYDROGEN BOND; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PEPTIDYL TRANSFER CATALYSIS; PH; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN HYDROLYSIS; PROTEIN SECRETION; PROTEIN SYNTHESIS; PROTEIN TRANSPORT; PROTON TRANSPORT; RIBOSOME; RNA TRANSLATION; STATIC ELECTRICITY;

EID: 79959411466     PISSN: 00664154     EISSN: 00664154     Source Type: Book Series    
DOI: 10.1146/annurev-biochem-082108-165150     Document Type: Article

References (124)

1. Johnson RM, Evans JD, Robinson GE, Berenbaum MR. 2009. Changes in transcript abundance relating to colony collapse disorder in honey bees (Apis mellifera). Proc. Natl. Acad. Sci. USA 106:14790-795.
2. Whitesides GM. 2001. The once and future nanomachine. Sci. Am. 285:78-83.
3. Savelsbergh A, Mohr D, Wilden B, Wintermeyer W, Rodnina MV. 2000. Stimulation of the GTPase activity of translation elongation factor G by ribosomal protein L7/12. J. Biol. Chem. 275:890-894. (Pubitemid 30051131)
4. Lill R, Robertson JM, WintermeyerW. 1989. Binding of the 3′ terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation. EMBO J. 8:3933-938. (Pubitemid 20016078)
5. Feinberg JS, Joseph S. 2001. Identification of molecular interactions between P-site tRNA and the ribosome essential for translocation. Proc. Natl. Acad. Sci. USA 98:11120-125. (Pubitemid 32928692)
6. Rodnina MV, Savelsbergh A, Katunin VI, Wintermeyer W. 1997. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385:37-41. (Pubitemid 27024544)
7. Pan D, Kirillov SV, Cooperman BS. 2007. Kinetically competent intermediates in the translocation step of protein synthesis. Mol. Cell 25:519-529. (Pubitemid 46274443)
8. Savelsbergh A, Katunin VI, Mohr D, Peske F, Rodnina MV, Wintermeyer W. 2003. An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol. Cell 11:1517-523. (Pubitemid 36776538)
9. Jencks WP. 1975. Binding energy, specificity, and enzymic catalysis: the circe effect. Adv. Enzymol. Relat. Areas Mol. Biol. 43:219-410.
10. Fersht A. 1999. Structure andMechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. New York: Freeman.
11. Krayevsky AA, Kukhanova MK. 1979. The peptidyltransferase center of ribosomes. Prog. Nucleic Acid Res. Mol. Biol. 23:1-51.
12. Sievers A, Beringer M, Rodnina MV, Wolfenden R. 2004. The ribosome as an entropy trap. Proc. Natl. Acad. Sci. USA 101:7897-901. (Pubitemid 38698025)
13. Pape T, Wintermeyer W, Rodnina MV. 1998. Complete kinetic mechanism of elongation factor Tudependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. EMBO J. 17:7490-497. (Pubitemid 29002715)
14. Bieling P, Beringer M, Adio S, Rodnina MV. 2006. Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat. Struct. Mol. Biol. 13:423-428. (Pubitemid 43881582)
15. Brunelle JL, Youngman EM, Sharma D, Green R. 2006. The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA 12:33-39. (Pubitemid 43037451)
16. Katunin VI, Muth GW, Strobel SA, Wintermeyer W, Rodnina MV. 2002. Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome. Mol. Cell 10:339-346. (Pubitemid 35007348)
17. Blackburn G, Jencks W. 1968. The mechanism of the aminolysis of methyl formate. J. Am. Chem. Soc. 90:2638-645.
18. Satterthwait A, Jencks W. 1974. Mechanism of aminolysis of acetate esters. J. Am. Chem. Soc. 96:7018-031.
19. Bilkadi Z, de Lorimier R, Kirsch JF. 1975. Secondary alpha-deuterium kinetic isotope effects and transition-state structures for the hydrolysis and hydrazinolysis reactions of formate esters. J. Am. Chem. Soc. 97:4317-322.
20. Sawyer CB, Kirsch JF. 1973. Kinetic isotope effects for reactions of methyl formate-methoxyl-18O. J. Am. Chem. Soc. 95:7375-381.
21. Marlier JF, Haptonstall BA, Johnson AJ, Sacksteder KA. 1997. Heavy-atom isotope effects on the hydrazinolysis of methyl formate. J. Am. Chem. Soc. 119:8838-842. (Pubitemid 27421369)
22. Sung DD, Koo IS, Yang K, Lee I. 2006. DFT studies on the structure and stability of zwitterionic tetrahedral intermediate in the aminolysis of esters. Chem. Phys. Lett. 426:280-284. (Pubitemid 44080151)
23. Singleton DA, Merrigan SR. 2000. Resolution of conflictingmechanistic observations in ester aminolysis. A warning on the qualitative prediction of isotope effects for reactive intermediates. J. Am. Chem. Soc. 122:11035-036.
24. Ilieva S, Galabov B, Musaev DG, Morokuma K, Schaefer HF. 2003. Computational study of the aminolysis of esters. The reaction of methylformate with ammonia. J. Org. Chem. 68:1496-502. (Pubitemid 36232514)
25. XiaX, Zhang C, Xue Y, Kim CK, YanG. 2008.DFTstudy andMonte Carlo simulation on the aminolysis of XC(O)OCH3 (X = NH2, H, and CF3) with monomeric and dimeric ammonias. J. Chem. Theory Comput. 4:1643-653.
26. Marlier JF, Haptonstall BA, Johnson AJ, Sacksteder KA. 1997. Heavy-atom isotope effects on the hydrazinolysis of methyl formate. J. Am. Chem. Soc. 119:838-842.
27. Marlier JF. 2001. Multiple isotope effects on the acyl group transfer reactions of amides and esters. Acc. Chem. Res. 34:283-290. (Pubitemid 32816465)
28. Hiller DA, ZhongM, Singh V, Strobel SA. 2010. Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects. Biochemistry 49:3868-78.
29. Seila AC, Okuda K, Nunez S, Seila AF, Strobel SA. 2005. Kinetic isotope effect analysis of the ribosomal peptidyl transferase reaction. Biochemistry 44:4018-027. (Pubitemid 40358054)
30. Kingery DA, Pfund E, Voorhees RM, Okuda K, Wohlgemuth I, et al. 2008. An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction. Chem. Biol. 15:493-500. (Pubitemid 351645115)
31. Okuda K, Seila AC, Strobel SA. 2005. Uncovering the enzymatic pKa of the ribosomal peptidyl transferase reaction utilizing a fluorinated puromycin derivative. Biochemistry 44:6675-684. (Pubitemid 40593818)
32. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. 2000. The structural basis of ribosome activity in peptide bond synthesis. Science 289:920-930. (Pubitemid 30659940)
33. Muth GW, Ortoleva-Donnelly L, Strobel SA. 2000. A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center. Science 289:947-950. (Pubitemid 30659946)
34. Hesslein AE, Katunin VI, Beringer M, Kosek AB, Rodnina MV, Strobel SA. 2004. Exploration of the conserved A+C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes. Nucleic Acids Res. 32:3760-770. (Pubitemid 39157723)
35. Bayfield MA, Thompson J, Dahlberg AE. 2004. The A2453-C2499 wobble base pair in Escherichia coli 23S ribosomal RNA is responsible for pH sensitivity of the peptidyltransferase active site conformation. Nucleic Acids Res. 32:5512-518. (Pubitemid 39545668)
36. Muth GW, Chen L, Kosek AB, Strobel SA. 2001. pH-dependent conformational flexibility within the ribosomal peptidyl transferase center. RNA 7:1403-415. (Pubitemid 32973226)
37. Xiong L, Polacek N, Sander P, B̈ottger EC, Mankin A. 2001. pKa of adenine 2451 in the ribosomal peptidyl transferase center remains elusive. RNA 7:1365-369. (Pubitemid 32973221)
38. Thompson J, Kim DF, O'Connor M, Lieberman KR, Bayfield MA, et al. 2001. Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit. Proc. Natl. Acad. Sci. USA 98:9002-7. (Pubitemid 32743859)
39. Polacek N, Gaynor M, Yassin A, Mankin AS. 2001. Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature 411:498-501. (Pubitemid 32494398)
40. Youngman EM, Brunelle JL, Kochaniak AB, Green R. 2004. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117:589-599. (Pubitemid 38692525)
41. Erlacher MD, Lang K, Shankaran N, Wotzel B, Huttenhofer A, et al. 2005. Chemical engineering of the peptidyl transferase center reveals an important role of the 2′-hydroxyl group of A2451. Nucleic Acids Res. 33:1618-627. (Pubitemid 41418389)
42. Beringer M, Adio S, WintermeyerW, RodninaM. 2003. TheG2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation. RNA 9:919-922. (Pubitemid 36899234)
43. Bevilacqua PC, Yajima R. 2006. Nucleobase catalysis in ribozyme mechanism. Curr. Opin. Chem. Biol. 10:455-464. (Pubitemid 44375067)
44. Knowles JR. 1976. The intrinsic pKa-values of functional groups in enzymes: improper deductions from the pH-dependence of steady-state parameters. CRC Crit. Rev. Biochem. 4:165-173.
45. Green R, Lorsch JR. 2002. The path to perdition is paved with protons. Cell 110:665-668. (Pubitemid 35283956)
46. Trobro S, Äqvist J. 2008. Role of ribosomal protein L27 in peptidyl transfer. Biochemistry 47:4898-906. (Pubitemid 351574996)
47. Wohlgemuth I, BeringerM, RodninaMV. 2006. Rapid peptide bond formation on isolated 50S ribosomal subunits. EMBO Rep. 7:699-703. (Pubitemid 43986266)
48. 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)
49. Schmeing TM, Huang KS, Strobel SA, Steitz TA. 2005. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438:520-524. (Pubitemid 41742026)
50. Schmeing TM, Seila AC, Hansen JL, Freeborn B, Soukup JK, et al. 2002. A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nat. Struct. Biol. 9:225-230. (Pubitemid 34171316)
51. Selmer M, Dunham CM, Murphy FV 4th, Weixlbaumer A, Petry S, et al. 2006. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313:1935-942. (Pubitemid 44497996)
52. Barta A, Steiner G, Brosius J, Noller HF, Kuechler E. 1984. Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center. Proc. Natl. Acad. Sci. USA 81:3607-611. (Pubitemid 14087774)
53. Noller HF, Hoffarth V, Zimniak L. 1992. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256:1416-419.
54. Bashan A, Agmon I, Zarivach R, Schluenzen F, Harms J, et al. 2003. Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression. Mol. Cell 11:91-102. (Pubitemid 36126593)
55. Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA. 2005. 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)
56. Hansen JL, Schmeing TM, Moore PB, Steitz TA. 2002. Structural insights into peptide bond formation. Proc. Natl. Acad. Sci. USA 99:11670-675. (Pubitemid 34994457)
57. Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, et al. 2001. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107:679-688. (Pubitemid 34014868)
58. Korostelev A, Trakhanov S, Laurberg M, Noller HF. 2006. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126:1065-077. (Pubitemid 44380300)
59. 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.
60. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, et al. 2005. Structures of the bacterial ribosome at 3.5 A resolution. Science 310:827-834. (Pubitemid 41567336)
61. Beringer M, Bruell C, Xiong L, Pfister P, Bieling P, et al. 2005. Essential mechanisms in the catalysis of peptide bond formation on the ribosome. J. Biol. Chem. 280:36065-072. (Pubitemid 41633877)
62. Bayfield MA, Dahlberg AE, Schulmeister U, Dorner S, Barta A. 2001. A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. Proc. Natl. Acad. Sci. USA 98:10096-101. (Pubitemid 32802980)
63. Chirkova A, Erlacher MD, Clementi N, Zywicki M, Aigner M, Polacek N. 2010. The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center. Nucleic Acids Res. 38:4844-855.
64. Trobro S, Äqvist J. 2005. Mechanism of peptide bond synthesis on the ribosome. Proc. Natl. Acad. Sci. USA 102:12395-400. (Pubitemid 41266370)
65. Trobro S, Äqvist J. 2006. Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer. Biochemistry 45:7049-056. (Pubitemid 43877393)
66. 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. 11:1101-6. (Pubitemid 39453339)
67. Erlacher MD, Lang K, Wotzel B, Rieder R, Micura R, Polacek N. 2006. Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2′-OH at A2451 of 23S rRNA. J. Am. Chem. Soc. 128:4453-459.
68. Bayryamov SG, Rangelov MA, Mladjova AP, Yomtova V, Petkov DD. 2007. Unambiguous evidence for efficient chemical catalysis of adenosine ester aminolysis by its 2′/3′-OH. J. Am. Chem. Soc. 129:5790-791. (Pubitemid 46748463)
69. Koch M, Huang Y, Sprinzl M. 2008. Peptide-bond synthesis on the ribosome: no free vicinal hydroxy group required on the terminal ribose residue of peptidyl-tRNA. Angew. Chem. Int. Ed. Engl. 47:7242-245.
70. Dall'Acqua W, Carter P. 2000. Substrate-assisted catalysis: molecular basis and biological significance. Protein Sci. 9:1-9. (Pubitemid 30070933)
71. Weinger JS, Strobel SA. 2006. Participation of the tRNA A76 hydroxyl groups throughout translation. Biochemistry 45:5939-948. (Pubitemid 43727085)
72. Rangelov MA, Vayssilov GN, Yomtova VM, Petkov DD. 2006. The syn-oriented 2-OH provides a favorable proton transfer geometry in 1, 2-diol monoester aminolysis: implications for the ribosome mechanism. J. Am. Chem. Soc. 128:4964-965.
73. Sharma PK, Xiang Y, Kato M, Warshel A. 2005. What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? Biochemistry 44:11307-314. (Pubitemid 41209066)
74. Schroeder GK, Wolfenden R. 2007. The rate enhancement produced by the ribosome: an improved model. Biochemistry 46:4037-044. (Pubitemid 46536067)
75. Huang KS, Carrasco N, Pfund E, Strobel SA. 2008. Transition state chirality and role of the vicinal hydroxyl in the ribosomal peptidyl transferase reaction. Biochemistry 47:8822-827.
76. Hashem Y, Auffinger P. 2009. A short guide formolecular dynamics simulations ofRNAsystems. Methods 47:187-197.
77. WallinG, Äqvist J. 2010. The transition state for peptide bond formation reveals the ribosome as a water trap. Proc. Natl. Acad. Sci. USA 107:1888-893.
78. Lang K, Erlacher M, Wilson DN, Micura R, Polacek N. 2008. The role of 23S ribosomal RNA residue A2451 in peptide bond synthesis revealed by atomic mutagenesis. Chem. Biol. 15:485-492. (Pubitemid 351645110)
79. Amort M, Wotzel B, Bakowska-Zywicka K, Erlacher MD, Micura R, Polacek N. 2007. An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination. Nucleic Acids Res. 35:5130-140. (Pubitemid 47394197)
80. Walter NG. 2007. Ribozyme catalysis revisited: Is water involved? Mol. Cell 28:923-929. (Pubitemid 350297026)
81. 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. 31:6536-542. (Pubitemid 37508758)
82. Das GK, Bhattacharyya D, Burma DP. 1999. A possible mechanism of peptide bond formation on ribosome without mediation of peptidyl transferase. J. Theor. Biol. 200:193-205. (Pubitemid 29481601)
83. Moazed D, Noller HF. 1989. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342:142-148. (Pubitemid 19277015)
84. Samaha RR, Green R, Noller HF. 1995. A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 377:309-314.
85. Kim DF, Green R. 1999. Base-pairing between 23S rRNA and tRNA in the ribosomal A site. Mol. Cell 4:859-864.
86. Eyring H, Polanyi M. 1931. On simple gas reactions. J. Phys. Chem. 12:279.
87. Wynne-Jones WFK, Eyring H. 1935. The absolute rate of reactions in condensed phases. J. Chem. Phys. 3:492-502.
88. Page MI, Jencks WP. 1971. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. Proc. Natl. Acad. Sci. USA 68:1678-683.
89. Westheimer FH. 1962. Mechanisms related to enzyme catalysis. Adv. Enzymol. Relat. Subj. Biochem. 24:441-482.
90. Villa J, Strajbl M, Glennon TM, Sham YY, Chu ZT, Warshel A. 2000. How important are entropic contributions to enzyme catalysis? Proc. Natl. Acad. Sci. USA 97:11899-904.
91. Wolfenden R, Snider M, Ridgway C, Miller B. 1999. The temperature dependence of enzyme rate enhancements. J. Am. Chem. Soc. 121:7419-420. (Pubitemid 29400173)
92. Johansson M, Bouakaz E, Lovmar M, Ehrenberg M. 2008. The kinetics of ribosomal peptidyl transfer revisited. Mol. Cell 30:589-598. (Pubitemid 351755061)
93. Rodriguez-Correa D, Dahlberg AE. 2008. Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus. RNA 14:2314-318.
94. Dunitz JD. 1995. Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions. Chem. Biol. 2:709-712.
95. CapecchiMR. 1967. Polypeptide chain termination in vitro: isolation of a release factor. Proc. Natl. Acad. Sci. USA 58:1144-151.
96. Scolnick E, Tompkins R, Caskey T, Nirenberg M. 1968. Release factors differing in specificity for terminator codons. Proc. Natl. Acad. Sci. USA 61:768-774.
97. Konecki DS, Aune KC, Tate W, Caskey CT. 1977. Characterization of reticulocyte release factor. J. Biol. Chem. 252:4514-520. (Pubitemid 8155968)
98. Moffat JG, Tate WP. 1994. A single proteolytic cleavage in release factor 2 stabilizes ribosome binding and abolishes peptidyl-tRNA hydrolysis activity. J. Biol. Chem. 269:18899-903. (Pubitemid 24226204)
99. Zavialov AV, Buckingham RH, EhrenbergM. 2001. A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107:115-124. (Pubitemid 32972042)
100. 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 125:1125-136. (Pubitemid 43866201)
101. Song H, Mugnier P, Das AK, Webb HM, Evans DR, et al. 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)
102. 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 8:1375-382. (Pubitemid 34085006)
103. 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.
104. Petry S, Brodersen DE, Murphy FV 4th, Dunham CM, Selmer M, et al. 2005. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell 123:1255-266. (Pubitemid 41821783)
105. Korostelev A, Laurberg M, Noller HF. 2009. Multistart simulated annealing refinement of the crystal structure of the 70S ribosome. Proc. Natl. Acad. Sci. USA 106:18195-200.
106. Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, et al. 2008. Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322:953-956.
107. SimonovicM, 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 14:2372-378.
108. AnderM, Äqvist J. 2009.Does glutaminemethylation affect the intrinsic conformation of the universally conserved GGQ motif in ribosomal release factors? Biochemistry 48:3483-489.
109. Trobro S, Äqvist 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)
110. Trobro S, Äqvist J. 2009.Mechanismof the translation termination reaction on the ribosome. Biochemistry 48:11296-303.
111. Caskey CT, Beaudet AL, Scolnick EM, Rosman M. 1971. Hydrolysis of fMet-tRNA by peptidyl transferase. Proc. Natl. Acad. Sci. USA 68:3163-167.
112. Shaw JJ, Green R. 2007. Two distinct components of release factor function uncovered by nucleophile partitioning analysis. Mol. Cell 28:458-467. (Pubitemid 350030565)
113. Zavialov AV, Mora L, Buckingham RH, EhrenbergM. 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)
114. Feinberg JS, Joseph S. 2006. A conserved base-pair between tRNA and 23 S rRNA in the peptidyl transferase center is important for peptide release. J. Mol. Biol. 364:1010-020. (Pubitemid 44765038)
115. Polacek N, Gomez MJ, Ito K, Xiong L, Nakamura Y, Mankin A. 2003. The critical role of the universally conserved A2602 of 23S ribosomal RNA in the release of the nascent peptide during translation termination. Mol. Cell 11:103-112. (Pubitemid 36126594)
116. Frolova LY, Tsivkovskii RY, Sivolobova GF, Oparina NY, Serpinsky OI, et al. 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 5:1014-020. (Pubitemid 29365331)
117. Mora L, Zavialov A, Ehrenberg M, Buckingham RH. 2003. Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli. Mol. Microbiol. 50:1467-476. (Pubitemid 38010445)
118. 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. 29:3982-987. (Pubitemid 32962688)
119. Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, et al. 2008. Crystal structure of a translation termination complex formed with release factor RF2. Proc. Natl. Acad. Sci. USA 105:19684-689.
120. 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 14:1526-531.
121. Schmeing TM, Voorhees RM, Kelley AC, Gao YG, Murphy FV 4th, et al. 2009. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326:688-694.
122. Steitz TA. 2008. A structural understanding of the dynamic ribosome machine. Nat. Rev. Mol. Cell Biol. 9:242-253. (Pubitemid 351301830)
123. Satterthwait AC, Jencks WP. 1974. Mechanism of aminolysis of acetate esters. J. Am. Chem. Soc. 96:7018-31.
124. 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. USA 107:8593-98