Home LiteratureArticle Details
PMID: 25594181 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Conformational changes of elongation factor G on the ribosome during tRNA translocation.

Cell ·Vol. 160 ·No. 1-2 ·2015-01-15 ·Pages 219-27

Lin J, Gagnon MG, Bulkley D, Steitz TA

Abstract

The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of EF-G in complex with the ribosome. Here, we report four atomic-resolution crystal structures of EF-G bound to the ribosome programmed in the pre- and posttranslocational states and to the ribosome trapped by the antibiotic dityromycin. We observe a previously unseen conformation of EF-G in the pretranslocation complex, which is independently captured by dityromycin on the ribosome. Our structures provide insights into the conformational space that EF-G samples on the ribosome and reveal that tRNA translocation on the ribosome is facilitated by a structural transition of EF-G from a compact to an elongated conformation, which can be prevented by the antibiotic dityromycin.

MeSH Terms
Depsipeptides/pharmacology Escherichia coli/chemistry,metabolism Models, Molecular Peptide Elongation Factor G/chemistry,metabolism RNA, Transfer/chemistry,metabolism Ribosomal Proteins/metabolism Ribosomes/chemistry,metabolism Thermus thermophilus/chemistry,metabolism X-Ray Diffraction
Chemicals
Depsipeptides Peptide Elongation Factor G Ribosomal Proteins dityromycin ribosomal protein L9 ribosomal protein S12 RNA, Transfer
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Lin Jinzhong
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
Gagnon Matthieu G
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.
Bulkley David
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
Steitz Thomas A
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA. Electronic address: thomas.steitz@yale.edu.
References (56)
56 references, click to expand
  1. Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
    Science. 2009 Aug 21;325(5943):966-70 PMID: 19696344
  2. Single-molecule structural dynamics of EF-G--ribosome interaction during translocation.
    Biochemistry. 2007 Sep 25;46(38):10767-75 PMID: 17727272
  3. mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
    Nat Struct Mol Biol. 2011 Apr;18(4):457-62 PMID: 21399643
  4. The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution.
    EMBO J. 1994 Aug 15;13(16):3661-8 PMID: 8070396
  5. Interactions of translational factor EF-G with the bacterial ribosome before and after mRNA translocation.
    J Mol Biol. 2004 Mar 12;337(1):15-30 PMID: 15001349
  6. Rotation of the head of the 30S ribosomal subunit during mRNA translocation.
    Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20391-4 PMID: 23188795
  7. The conformational properties of elongation factor G and the mechanism of translocation.
    Biochemistry. 1997 Aug 19;36(33):10327-34 PMID: 9254632
  8. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation.
    Mol Cell. 2008 May 9;30(3):348-59 PMID: 18471980
  9. Phaser crystallographic software.
    J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674 PMID: 19461840
  10. Following movement of domain IV of elongation factor G during ribosomal translocation.
    Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15060-5 PMID: 25288752
  11. Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation.
    Proc Natl Acad Sci U S A. 1998 May 26;95(11):6134-8 PMID: 9600930
  12. GTPase activation of elongation factors Tu and G on the ribosome.
    Biochemistry. 2002 Oct 15;41(41):12520-8 PMID: 12369843
  13. Locking and unlocking of ribosomal motions.
    Cell. 2003 Jul 11;114(1):123-34 PMID: 12859903
  14. Identification of two distinct hybrid state intermediates on the ribosome.
    Mol Cell. 2007 Feb 23;25(4):505-17 PMID: 17317624
  15. The structure of the ribosome with elongation factor G trapped in the posttranslocational state.
    Science. 2009 Oct 30;326(5953):694-9 PMID: 19833919
  16. Structure of the ribosome with elongation factor G trapped in the pretranslocation state.
    Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):20994-9 PMID: 24324137
  17. An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation.
    Mol Cell. 2003 Jun;11(6):1517-23 PMID: 12820965
  18. Crystal structure of a mutant elongation factor G trapped with a GTP analogue.
    FEBS Lett. 2005 Aug 15;579(20):4492-7 PMID: 16083884
  19. Control of phosphate release from elongation factor G by ribosomal protein L7/12.
    EMBO J. 2005 Dec 21;24(24):4316-23 PMID: 16292341
  20. Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome.
    EMBO J. 2009 Jul 22;28(14):2053-65 PMID: 19536129
  21. Elongation factor G bound to the ribosome in an intermediate state of translocation.
    Science. 2013 Jun 28;340(6140):1235490 PMID: 23812720
  22. Interaction of thiostrepton and elongation factor-G with the ribosomal protein L11-binding domain.
    J Biol Chem. 2005 Jan 28;280(4):2934-43 PMID: 15492007
  23. Coordinated conformational and compositional dynamics drive ribosome translocation.
    Nat Struct Mol Biol. 2013 Jun;20(6):718-27 PMID: 23624862
  24. Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome.
    Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9586-90 PMID: 10449736
  25. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
    Mol Cell. 2007 Mar 9;25(5):751-64 PMID: 17349960
  26. Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.
    Science. 2012 Mar 16;335(6074):1370-2 PMID: 22422986
  27. The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.
    Cell Rep. 2014 Jan 30;6(2):357-65 PMID: 24412368
  28. A ratchet-like inter-subunit reorganization of the ribosome during translocation.
    Nature. 2000 Jul 20;406(6793):318-22 PMID: 10917535
  29. Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome.
    RNA. 2001 Dec;7(12):1879-85 PMID: 11780642
  30. Structural basis of the translational elongation cycle.
    Annu Rev Biochem. 2013;82:203-36 PMID: 23746255
  31. Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex.
    Mol Cell. 2003 Aug;12(2):321-8 PMID: 14536072
  32. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
    Nature. 2010 Dec 2;468(7324):713-6 PMID: 21124459
  33. PHENIX: building new software for automated crystallographic structure determination.
    Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54 PMID: 12393927
  34. Structural and functional characterization of the bacterial translocation inhibitor GE82832.
    FEBS Lett. 2012 Sep 21;586(19):3373-8 PMID: 22841550
  35. Kinetically competent intermediates in the translocation step of protein synthesis.
    Mol Cell. 2007 Feb 23;25(4):519-29 PMID: 17317625
  36. Characterization of GE82832, a peptide inhibitor of translocation interacting with bacterial 30S ribosomal subunits.
    RNA. 2006 Jul;12(7):1262-70 PMID: 16699167
  37. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.
    Nat Struct Mol Biol. 2009 May;16(5):528-33 PMID: 19363482
  38. Spontaneous intersubunit rotation in single ribosomes.
    Mol Cell. 2008 Jun 6;30(5):578-88 PMID: 18538656
  39. Structure of EF-G-ribosome complex in a pretranslocation state.
    Nat Struct Mol Biol. 2013 Sep;20(9):1077-84 PMID: 23912278
  40. Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation.
    Cell. 2000 Feb 4;100(3):301-9 PMID: 10676812
  41. Correlated conformational events in EF-G and the ribosome regulate translocation.
    Nat Struct Mol Biol. 2010 Dec;17(12):1470-7 PMID: 21057527
  42. Thiostrepton inhibits stable 70S ribosome binding and ribosome-dependent GTPase activation of elongation factor G and elongation factor 4.
    Nucleic Acids Res. 2012 Jan;40(1):360-70 PMID: 21908407
  43. Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation.
    Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):20964-9 PMID: 24324168
  44. Control of ribosomal subunit rotation by elongation factor G.
    Science. 2013 Jun 28;340(6140):1235970 PMID: 23812721
  45. GTP hydrolysis by EF-G synchronizes tRNA movement on small and large ribosomal subunits.
    EMBO J. 2014 May 2;33(9):1073-85 PMID: 24614227
  46. Coot: model-building tools for molecular graphics.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32 PMID: 15572765
  47. The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
    Nat Struct Mol Biol. 2010 Mar;17(3):289-93 PMID: 20154709
  48. How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation.
    Science. 2014 Sep 5;345(6201):1188-91 PMID: 25190797
  49. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome.
    Science. 2014 Aug 8;345(6197):684-7 PMID: 25104389
  50. Domain III of elongation factor G from Thermus thermophilus is essential for induction of GTP hydrolysis on the ribosome.
    J Biol Chem. 2000 Nov 17;275(46):35820-4 PMID: 10940297
  51. Elongation factor G stabilizes the hybrid-state conformation of the 70S ribosome.
    RNA. 2007 Sep;13(9):1473-82 PMID: 17630323
  52. Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.
    Science. 2013 Jun 28;340(6140):1236086 PMID: 23812722
  53. EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome.
    Nat Struct Biol. 1999 Jul;6(7):643-7 PMID: 10404220
  54. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome.
    Nature. 1997 Jan 2;385(6611):37-41 PMID: 8985244
  55. Single-molecule fluorescence measurements of ribosomal translocation dynamics.
    Mol Cell. 2011 May 6;42(3):367-77 PMID: 21549313
  56. tRNA dynamics on the ribosome during translation.
    Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12893-8 PMID: 15317937
Article Info
Journal
Cell
Abbr.
Cell
ISSN
1097-4172
DOI
10.1016/j.cell.2014.11.049
Email
thomas.steitz@yale.edu
Published
2015-01-15
Pages
219-27
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC4297320
Subset
IM
Grants
Howard Hughes Medical Institute · United States
NIBIB NIH HHS · P30 EB009998 · United States
NIGMS NIH HHS · P41 GM111244 · United States
NIGMS NIH HHS · P01 GM022778 · United States
NIGMS NIH HHS · GM022778 · United States
External Links
PubMed source DOI: 10.1016/j.cell.2014.11.049 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2