Особенности активации гидролитической активности факторов элонгации

Аннотация

Трансляционные ГТФазы (трГТФазы), относящиеся к классу G-белков, играют ключевую роль на всех этапах биосинтеза белка на рибосоме. Однонаправ­ленность и цикличность функциони­рования G-белков обеспечивается возможностью их переключения между активным и неактивным состояниями вследствие гидролиза ГТФ, ускоряемого вспомогатель­ными белками-стимуляторами ГТФазной активности. Несмотря на то что трГТФазы взаимодействуют с рибосомами, находящимися в разных конформа­ционных состояниях, для активации они связываются с одной и той же консервативной областью, которая, в отличие от классических белков-стимуляторов ГТФазной активности, представлена РНК. В результате у всех факторов элонгации образуется практически одинаковая структура активного катали­тического центра, предполагающая единый механизм реакции гидролиза ГТФ. Однако нюансы в процессе формирования активированного состояния, а также существенно отличающаяся скорость реакции гидролиза ГТФ указывают на существование особенностей при реализации гидролити­ческой функции разными факторами элонгации. В данной работе представлено современное видение механизмов регулирования ГТФазной активности факторов элонгации EF-Tu, EF-G и SelB и гидролиза ГТФ, основанное на анализе структурных, биохимических и биоинформа­тических данных.

Сноски

* Адресат для корреспонденции.

Финансирование

Работа выполнена при финансовой поддержке Российского научного фонда (грант № 17-14-01416).

Благодарности

Мы благодарим за плодотворные дискуссии всех сотрудников лаборатории биосинтеза белка ОМРБ НИЦ «КИ» – ПИЯФ.

Конфликт интересов

Авторы заявляют об отсутствии конфликта интересов.

Соблюдение этических норм

Настоящая статья не содержит описания каких-либо исследований с участием людей или животных в качестве объектов.

Список литературы

1. Schmeing, T. M., and Ramakrishnan, V. (2009) What recent ribosome structures have revealed about the mechanism of translation, Nature, 461, 1234-1242, doi: 10.1038/nature08403.

2. Maracci, C., and Rodnina, M. V. (2016) Review: translational GTPases, Biopolymers, 105, 463-475, doi: 10.1002/bip.22832.

3. Atkinson, C. G. (2015) The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life, BMC Genomics, 16, 78, doi: 10.1186/s12864-015-1289-7.

4. Bourne, H. R., Sanders, D. A., and McCormick, F. (1991) The GTPase superfamily: conserved structure and molecular mechanism, Nature, 349, 117-127, doi: 10.1038/349117a0.

5. Vetter, I. R., Nowak, C., Nishimoto, T., Kuhlmann, J., and Wittinghofer, A. (1999) Structure of a ran-binding domain complexed with ran bound to a GTP analogue: implications for nuclear transport, Nature, 398, 39-46, doi: 10.1038/17969.

6. Hilgenfeld, R. (1995) Regulatory GTPases, Curr. Opin. Struct. Biol., 5, 810-817, doi: 10.1016/0959-440X(95)80015-8.

7. Scheffzek, K., Ahmadian, M. R., Kabsch, W., Wiesmüller, L., Lautwein, A., Schmitz, F., and Wittinghofer, A. (1997) The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic ras mutants, Science, 277, 333-338, doi: 10.1126/science.277.5324.333.

8. Wittinghofer, A., Scheffzek, K., and Ahmadian, M. R. (1997) The Interaction of ras with GTPase-activating proteins, FEBS Lett., 410, 63-67, doi: 10.1016/S0014-5793(97)00321-9.

9. Vetter, I. R., and Wittinghofer, A. (2001) The guanine nucleotide-binding switch in three dimensions, Science, 294, 1299-1304, doi: 10.1126/science.1062023.

10. Ævarsson, A. (1995) Structure-based sequence alignment of elongation factors Tu and G with related GTPases involved in translation, J. Mol. Evol., 41, 1096-104, doi: 10.1007/BF00173191.

11. Daviter, T., Wieden, H. J., and Rodnina, M. V. (2003) Essential role of histidine 84 in elongation factor Tu for the chemical step of GTP hydrolysis on the ribosome, J. Mol. Biol., 332, 689-699, doi: 10.1016/S0022-2836(03)00947-1.

12. Maracci, C., Peske, F., Dannies, E., Pohl, C., and Rodnina, M. V. (2014) Ribosome-induced tuning of GTP hydrolysis by a translational GTPase, Proc. Natl. Acad. Sci. USA, 111, 14418-14423, doi: 10.1073/pnas.1412676111.

13. Koripella, R. K., Holm, M., Dourado, D., Mandava, C. S., Flores, S., and Sanyal, S. (2015) A conserved histidine in switch-II of EF-G moderates release of inorganic phosphate, Sci. Rep., 5, doi: 10.1038/srep12970.

14. Cunha, C. E., Belardinelli, R., Peske, F., Holtkamp, W., Wintermeyer, W., and Rodnina, M. V. (2013) Dual use of GTP hydrolysis by elongation factor G on the ribosome, Translation, 1, e24315-11, doi: 10.4161/trla.24315.

15. Zeidler, W., Egle, C., Ribeiro, S., Wagner, A., Katunin, V., Kreutzer, R., Rodnina, M., Wintermeyer, W., and Sprinzl, M. (1995) Site-directed mutagenesis of Thermus Thermophilus elongation factor Tu: replacement of His85, Asp81 and Arg300, Eur. J. Biochem., 229, 596-604, doi: 10.1111/j.1432-1033.1995.0596j.x.

16. Scarano, G., Krab, I. M., Bocchini, V., and Parmeggiani, A. (1995) Relevance of histidine-84 in the elongation factor Tu GTPase activity and in poly(Phe) synthesis: its substitution by glutamine and alanine, FEBS Lett., 365, 214-218, doi: 10.1016/0014-5793(95)00469-P.

17. Voorhees, R. M., Schmeing, T. M., Kelley, A. C., and Ramakrishnan, V. (2010) The mechanism for activation of GTP hydrolysis on the ribosome, Science, 330, 835-838, doi: 10.1126/science.1194460.

18. Chen, Y., Feng, S., Kumar, V., Ero, R., and Gao, Y. G. (2013) Structure of EF-G-ribosome complex in a pretranslocation state, Nat. Struct. Mol. Biol., 20, 1077-1084, doi: 10.1038/nsmb.2645.

19. Tourigny, D. S., Fernández, I. S., Kelley, A. C., and Ramakrishnan, V. (2013) Elongation factor G bound to the ribosome in an intermediate state of translocation, Science, 340, 1235490–1235497, doi: 10.1126/science.1235490.

20. Fischer, N., Neumann, P., Bock, L. V., Maracci, C., Wang, Z., Paleskava, A., Konevega, A.L., Schröder, G. F., Grubmüller, H., Ficner, R., Rodnina, M. V., and Stark, H. (2016) The pathway to GTPase activation of elongation factor SelB on the ribosome, Nature, 540, 80-85, doi: 10.1038/nature20560.

21. Loveland, A. B., Demo, G., and Korostelev, A. A. (2020) Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates TRNA proofreading, Nature, 584, 640-645, doi: 10.1038/s41586-020-2447-x.

22. Loveland, A. B., Demo, G., Grigorieff, N., and Korostelev, A. A. (2017) Ensemble Cryo-EM elucidates the mechanism of translation fidelity, Nature, 546, 113-117, doi: 10.1038/nature22397.

23. Fischer, N., Neumann, P., Konevega, A. L., Bock, L. V., Ficner, R., Rodnina, M. V., and Stark, H. (2015) Structure of the E. Coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected Cryo-EM, Nature, 520, 567-570, doi: 10.1038/nature14275.

24. Liljas, A., Ehrenberg, M., and Åqvist, J. (2011) Comment on “The mechanism for activation of GTP hydrolysis on the ribosome”, Science, 333, 37, doi: 10.1126/science.1202472.

25. Wallin, G., Kamerlin, S. C. L., and Åqvist, J. (2013) Energetics of activation of GTP hydrolysis on the ribosome, Nat. Commun., 4, 1733, doi: 10.1038/ncomms2741.

26. Li, W., Liu, Z., Koripella, R. K., Langlois, R., Sanyal, S., and Frank, J. (2015) Activation of GTP hydrolysis in MRNA-TRNA translocation by elongation factor G, Sci. Adv., 1, e1500169-7, doi: 10.1126/sciadv.1500169.

27. Mercier, E., Girodat, D., and Wieden, H. J. (2015) A Conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu, Sci. Rep., 5, doi: 10.1038/srep07677.

28. Shi, X., Khade, P. K., Sanbonmatsu, K. Y., and Joseph, S. (2012) Functional role of the sarcin-ricin loop of the 23s RRNA in the elongation cycle of protein synthesis, J. Mol. Biol., 419, 125-138, doi: 10.1016/j.jmb.2012.03.016.

29. Mitkevich, V. A., Shyp, V., Petrushanko, I. Y., Soosaar, A., Atkinson, G. C., Tenson, T., Makarov, A. A., and Hauryliuk, V. (2012) GTPases IF2 and EF-G bind GDP and the SRL RNA in a mutually exclusive manner, Sci. Rep., 2, 843, doi: 10.1038/srep00843.

30. Clementi, N., Chirkova, A., Puffer, B., Micura, R., and Polacek, N. (2010) Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation, Nat. Chem. Biol., 6, 344-351, doi: 10.1038/nchembio.341.

31. Moazed, D., Robertson, J. M., and Noller, H. F. (1988) Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA, Nature, 334, 362-364, doi: 10.1038/334362a0.

32. Stark, H., Rodnina, M. V., Wieden, H. J., Zemlin, F., Wintermeyer, W., and Van Heel, M. (2002) Ribosome interactions of aminoacyl-TRNA and elongation factor Tu in the codon-recognition complex, Nat. Struct. Biol., 9, 849-854, doi: 10.1038/nsb859.

33. Lin, J., Gagnon, M. G., Bulkley, D., and Steitz, T. A. (2015) Conformational changes of elongation factor G on the ribosome during TRNA translocation, Cell, 160, 219-227, doi: 10.1016/j.cell.2014.11.049.

34. Voorhees, R. M., Schmeing, T. M., Kelley, A. C., and Ramakrishnan, V. (2011) Response to comment on “The mechanism for activation of GTP hydrolysis on the ribosome”, Science, 333, 37, doi: 10.1126/science.1202532.

35. Kirby, A. J., and Jencks, W. P. (1965) The reactivity of nucleophilic reagents toward the P-nitrophenyl phosphate dianion, J. Am. Chem. Soc., 87, 3209-3216, doi: 10.1021/ja01092a036.

36. Paleskava, A., Konevega, A. L., and Rodnina, M. V. (2012) Thermodynamics of the GTP-GDP-operated conformational switch of selenocysteine-specific translation factor SelB, J. Biol. Chem., 287, 27906-27912, doi: 10.1074/jbc.M112.366120.

37. Leibundgut, M., Frick, C., Thanbichler, M., Böck, A., and Ban, N. (2005) Selenocysteine TRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors, EMBO J., 24, 11-22, doi: 10.1038/sj.emboj.7600505.

38. Klähn, M., Rosta, E., and Warshel, A. (2006) On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins, J. Am. Chem. Soc., 128, 15310-15323, doi: 10.1021/ja065470t.

39. Åqvist, J., Kolmodin, K., Florian, J., and Warshel, A. (1999) Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data? Chem. Biol., 6, 71-80, doi: 10.1016/S1074-5521(99)89003-6.

40. Berchtold, H., Reshetnikova, L., Reiser, C. O. A., Schirmer, N. K., Sprinzl, M., and Hilgenfeld, R. (1993) Crystal structure of active elongation factor Tu reveals major domain rearrangements, Nature, 365, 126-132, doi: 10.1038/365126a0.

41. Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B. F. C., and Nyborg, J. (1995) Crystal structure of the ternary complex of Phe-TRNAPhe, EF-Tu, and a GTP analog, Science, 270, 1464-1472, doi: 10.1126/science.270.5241.1464.

42. Fislage, M., Zhang, J., Brown, Z. P., Mandava, C. S., Sanyal, S., Ehrenberg, M., and Frank, J. (2018) Cryo-EM shows stages of initial codon selection on the ribosome by Aa-TRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A, Nucleic Acids Res., 46, 5861-5874, doi: 10.1093/nar/gky346.

43. Rodnina, M. V., Fricke, R., Kuhn, L., and Wintermeyer, W. (1995) Codon-dependent conformational change of elongation factor Tu preceding GTP hydrolysis on the ribosome, EMBO J., 14, 2613-2619, doi: 10.1002/j.1460-2075.1995.tb07259.x.

44. Pape, T., Wintermeyer, W., and Rodnina, M. V. (1998) Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-TRNA to the A site of the E. Coli ribosome, EMBO J., 17, 7490-7497, doi: 10.1093/emboj/17.24.7490.

45. Yang, H., Perrier, J., and Whitford, P. C. (2018) Disorder guides domain rearrangement in elongation factor Tu, Proteins, 86, 1037-1046, doi: 10.1002/prot.25575.

46. Abel, K., Yoder, M. D., Hilgenfeld, R., and Jurnak, F. (1996) An α to β conformational switch in EF-Tu, Structure, 4, 1153-1159, doi: 10.1016/S0969-2126(96)00123-2.

47. Gromadski, K. B., Wieden, H. J., and Rodnina, M. V. (2002) Kinetic mechanism of elongation factor Ts-catalyzed nucleotide exchange in elongation factor Tu, Biochemistry, 41, 162-169, doi: 10.1021/bi015712w.

48. AEvarsson, A., Brazhnikov, E., Garber, M., Zheltonosova, J., Chirgadze, Y., Al-Karadaghi, S., Svensson, L. A., and Liljas, A. (1994) Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus Thermophilus, EMBO J., 13, 3669-3677, doi: 10.1002/j.1460-2075.1994.tb06676.x.

49. Janosi, L., Hara, H., Zhang, S., and Kaji, A. (1996) Ribosome recycling by ribosome recycling factor (RRF) – an important but overlooked step of protein biosynthesis, Adv. Biophys., 32, 121-201, doi: 10.1016/0065-227X(96)84743-5.

50. Margus, T., Remm, M., and Tenson, T. (2011) A computational study of elongation factor G (EFG) duplicated genes: diverged nature underlying the innovation on the same structural template, PLoS One, 6, e22789, doi: 10.1371/journal.pone.0022789.

51. Rodnina, M. V., Savelsbergh, A., Katunin, V. I., and Wintermeyer, W. (1997) Hydrolysis of GTP by elongation factor G drives TRNA movement on the ribosome, Nature, 385, 37-41, doi: 10.1038/385037a0.

52. Wilden, B., Savelsbergh, A., Rodnina, M. V., and Wintermeyer, W. (2006) Role and timing of GTP binding and hydrolysis during EF-G-dependent TRNA translocation on the ribosome, Proc. Natl. Acad. Sci. USA, 103, 13670-13675, doi: 10.1073/pnas.0606099103.

53. Kromayer, M., Wilting, R., Tormay, P., and Böck, A. (1996) Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB, J. Mol. Biol., 262, 413-420, doi: 10.1006/jmbi.1996.0525.

54. Thanbichler, M., Böck, A., and Goody, R. S. (2000) Kinetics of the interaction of translation factor SelB from Escherichia Coli with guanosine nucleotides and selenocysteine insertion sequence RNA, J. Biol. Chem., 275, 20458-20466, doi: 10.1074/jbc.M002496200.

55. Paleskava, A., Konevega, A. L., and Rodnina, M. V. (2010) Thermodynamic and kinetic framework of selenocysteyl-TRNASec recognition by elongation factor SelB, J. Biol. Chem., 285, 3014-3020, doi: 10.1074/jbc.M109.081380.

56. Kjeldgaard, M., Nissen, P., Thirup, S., and Nyborg, J. (1993) The Crystal structure of elongation factor EF-Tu from Thermus Aquaticus in the GTP conformation, Structure, 1, 35-50, doi: 10.1016/0969-2126(93)90007-4.

57. Hilgenfeld, R. (2000) Insights into the GTPase mechanism of EF-Tu from structural studies, in: The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions, (Garrett, R., ed.), Washington, DC, pp. 347-357.

58. Hansson, S., Singh, R., Gudkov, A. T., Liljas, A., and Logan, D. T. (2005) Crystal structure of a mutant elongation factor G trapped with a GTP analogue, FEBS Lett., 579, 4492-4497, doi: 10.1016/j.febslet.2005.07.016.

59. Itoh, Y., Sekine, S. I., and Yokoyama, S. (2015) Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB, Nucleic Acids Res., 43, 9028-9038, doi: 10.1093/nar/gkv833.

60. Czworkowski, J., Wang, J., Steitz, T. A., and Moore, P. B. (1994) The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution, EMBO J., 13, 3661-3668, doi: 10.1002/j.1460-2075.1994.tb06675.x.

61. Hansson, S., Singh, R., Gudkov, A. T., Liljas, A., and Logan, D. T. (2005) Structural insights into fusidic acid resistance and sensitivity in EF-G, J. Mol. Biol., 348, 939-949, doi: 10.1016/j.jmb.2005.02.066.

62. Fasano, O., De Vendittis, E., and Parmeggiani, A. (1982) Hydrolysis of GTP by elongation factor Tu can be induced by monovalent cations in the absence of other effectors, J. Biol. Chem., 257, 3145-3150.

63. Kuhle, B., and Ficner, R. (2014) A monovalent cation acts as structural and catalytic cofactor in translational GTP ases, EMBO J., 33, 2547-2563, doi: 10.15252/embj.201488517.

64. Gao, Y. G., Selmer, M., Dunham, C. M., Weixlbaumer, A., Kelley, A. C., and Ramakrishnan, V. (2009) The structure of the ribosome with elongation factor G trapped in the posttranslocational state, Science, 326, 694-699, doi: 10.1126/science.1179709.

65. LaRiviere, F. J., Wolfson, A. D., and Uhlenbeck, O. C. (2001) Uniform binding of aminoacyl-TRNAs to elongation factor Tu by thermodynamic compensation, Science, 294, 165-168, doi: 10.1126/science.1064242.

66. Mittelstaet, J., Konevega, A. L., and Rodnina, M. V. (2011) Distortion of TRNA upon near-cognate codon recognition on the ribosome, J. Biol. Chem., 286, 8158-8164, doi: 10.1074/jbc.M110.210021.

67. Valle, M., Sengupta, J., Swami, N. K., Grassucci, R. A., Burkhardt, N., Nierhaus, K. H., Agrawal, R. K., and Frank, J. (2002) Cryo-EM reveals an active role for aminoacyl-TRNA in the accommodation process, EMBO J., 21, 3557-3567, doi: 10.1093/emboj/cdf326.

68. Schmeing, M. T., Voorhees, R. M., Kelley, A. C., Gao, Y. G., Murphy IV, F. V., Weir, J.R., and Ramakrishnan, V. (2009) The crystal structure of the ribosome bound to EF-Tu and aminoacyl-TRNA, Science, 326, 688-694, doi: 10.1126/science.1179700.

69. Vetter, I. R., and Wittinghofer, A. (1999) Nucleoside triphosphate-binding proteins: different scaffolds to achieve phosphoryl transfer, Q. Rev. Biophys., 32, 1-56, doi: 10.1017/S0033583599003480.

70. Kötting, C., Blessenohl, M., Suveyzdis, Y., Goody, R. S., Wittinghofer, A., and Gerwert, K. (2006) A phosphoryl transfer intermediate in the GTPase reaction of Ras in complex with its GTPase-activating protein, Proc. Natl. Acad. Sci. USA, 103, 13911-13916, doi: 10.1073/pnas.0604128103.

71. Pasqualato, S., and Cherfils, J. (2005) Crystallographic evidence for substrate-assisted GTP hydrolysis by a small GTP binding protein, Structure, 13, 533-540, doi: 10.1016/j.str.2005.01.014.

72. Schweins, T., Geyer, M., Scheffzek, K., Warshel, A., Kalbitzer, H. R., and Wittinghofer, A. (1995) Substrate-assisted catalysis as a mechanism for Gtp hydrolysis of P21ras and other GTP-binding proteins, Nat. Struct. Biol., 2, 36-44, doi: 10.1038/nsb0195-36.

73. Kothe, U., and Rodnina, M. V. (2006) Delayed release of inorganic phosphate from elongation factor Tu following GTP hydrolysis on the ribosome, Biochemistry, 45, 12767-12774, doi: 10.1021/bi061192z.

74. Savelsbergh, A., Mohr, D., Kothe, U., Wintermeyer, W., and Rodnina, M. V. (2005) Control of phosphate release from elongation factor G by ribosomal protein L7/12, EMBO J., 24, 4316-4323, doi: 10.1038/sj.emboj.7600884.

75. Zhou, J., Lancaster, L., Donohue, J. P., and Noller, H. F. (2013) Crystal structures of EF-G – ribosome complexes trapped in intermediate states of translocation, Science, 340, 1236086, doi: 10.1126/science.1236086.

76. Koch, M., Flür, S., Kreutz, C., Ennifar, E., Micura, R., and Polacek, N. (2015) Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered GTP hydrolysis, Proc. Natl. Acad. Sci. USA, 112, E2561-E2568, doi: 10.1073/pnas.1505231112.

77. Sondek, J., Lambright, D. G., Noel, J. P., Hamm, H. E., and Sigler, P. B. (1994) GTPase mechanism of Gproteins from the 1.7-Å crystal structure of transducin α-GGDP-AIF-4, Nature, 372, 276-279, doi: 10.1038/372276a0.

78. Adamczyk, A. J., and Warshel, A. (2011) Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome, Proc. Natl. Acad. Sci. USA, 108, 9827-9832, doi: 10.1073/pnas.1105714108.

79. Prasad, B. R., Plotnikov, N. V., Lameira, J., and Warshel, A. (2013) Quantitative exploration of the molecular origin of the activation of GTPase, Proc. Natl. Acad. Sci. USA, 110, 20509-20514, doi: 10.1073/pnas.1319854110.

80. Doudna, J. A., and Lorsch, J. R. (2005) Ribozyme catalysis: not different, just worse, Nat. Struct. Mol. Biol., 12, 395-402, doi: 10.1038/nsmb932.