Elongation factor 4 remodels the A-site tRNA on the ribosome
Abstract
During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. Furthermore, the structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.
- Authors:
-
- Yale Univ., New Haven, CT (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; National Inst. of Health
- OSTI Identifier:
- 1255296
- Grant/Contract Number:
- AC02-06CH11357; GM022778; P41 GM103403; S10 RR029205
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Volume: 113; Journal Issue: 18; Journal ID: ISSN 0027-8424
- Publisher:
- National Academy of Sciences
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; elongation factor 4; ribosome; tRNA; remodeling; protein–RNA interactions
Citation Formats
Gagnon, Matthieu G., Lin, Jinzhong, and Steitz, Thomas A. Elongation factor 4 remodels the A-site tRNA on the ribosome. United States: N. p., 2016.
Web. doi:10.1073/pnas.1522932113.
Gagnon, Matthieu G., Lin, Jinzhong, & Steitz, Thomas A. Elongation factor 4 remodels the A-site tRNA on the ribosome. United States. https://doi.org/10.1073/pnas.1522932113
Gagnon, Matthieu G., Lin, Jinzhong, and Steitz, Thomas A. Mon .
"Elongation factor 4 remodels the A-site tRNA on the ribosome". United States. https://doi.org/10.1073/pnas.1522932113. https://www.osti.gov/servlets/purl/1255296.
@article{osti_1255296,
title = {Elongation factor 4 remodels the A-site tRNA on the ribosome},
author = {Gagnon, Matthieu G. and Lin, Jinzhong and Steitz, Thomas A.},
abstractNote = {During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. Furthermore, the structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.},
doi = {10.1073/pnas.1522932113},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 18,
volume = 113,
place = {United States},
year = {Mon Apr 18 00:00:00 EDT 2016},
month = {Mon Apr 18 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 16 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Interrupted Catalysis: The EF4 (LepA) Effect on Back-Translocation
journal, March 2010
- Liu, Hanqing; Pan, Dongli; Pech, Markus
- Journal of Molecular Biology, Vol. 396, Issue 4
GTPase Mechanisms and Functions of Translation Factors on the Ribosome
journal, January 2000
- Rodnina, M. V.; Stark, H.; Savelsbergh, A.
- Biological Chemistry, Vol. 381, Issue 5-6
Crystal Structures of EF-G–Ribosome Complexes Trapped in Intermediate States of Translocation
journal, June 2013
- Zhou, Jie; Lancaster, Laura; Donohue, John Paul
- Science, Vol. 340, Issue 6140
Ribosome-associated GTPases: The role of RNA for GTPase activation
journal, September 2010
- Clementi, Nina; Polacek, Norbert
- RNA Biology, Vol. 7, Issue 5
Elongation Factor G Bound to the Ribosome in an Intermediate State of Translocation
journal, June 2013
- Tourigny, David S.; Fernández, Israel S.; Kelley, Ann C.
- Science, Vol. 340, Issue 6140
Elongation factor 4 (EF4/LepA) accelerates protein synthesis at increased Mg2+ concentrations
journal, February 2011
- Pech, M.; Karim, Z.; Yamamoto, H.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 8
Control of Ribosomal Subunit Rotation by Elongation Factor G
journal, June 2013
- Pulk, Arto; Cate, Jamie H. D.
- Science, Vol. 340, Issue 6140
Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3
journal, September 2011
- Jin, H.; Kelley, A. C.; Ramakrishnan, V.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 38, p. 15798-15803
In Vivo Deuteration of Transfer RNAs: Overexpression and Large-Scale Purification of Deuterated Specific tRNAs
journal, January 1996
- Junemann, R.; Wadzack, J.; Triana-Alonso, F. J.
- Nucleic Acids Research, Vol. 24, Issue 5
The paradox of elongation factor 4: highly conserved, yet of no physiological significance?
journal, May 2013
- Zhang, Dejiu; Qin, Yan
- Biochemical Journal, Vol. 452, Issue 2
Translational termination comes of age
journal, November 2000
- Kisselev, Lev L.; Buckingham, Richard H.
- Trends in Biochemical Sciences, Vol. 25, Issue 11
Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome
journal, December 2011
- Zhou, J.; Lancaster, L.; Trakhanov, S.
- RNA, Vol. 18, Issue 2
Ribosomal Elongation Factor 4 Promotes Cell Death Associated with Lethal Stress
journal, December 2014
- Li, Liping; Hong, Yuzhi; Luan, Gan
- mBio, Vol. 5, Issue 6
Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites
journal, May 1989
- Moazed, Danesh; Noller, Harry F.
- Cell, Vol. 57, Issue 4
The conserved protein EF4 (LepA) modulates the elongation cycle of protein synthesis
journal, September 2011
- Liu, H.; Chen, C.; Zhang, H.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 39
Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit
journal, May 2001
- Ogle, J. M.
- Science, Vol. 292, Issue 5518
Structural insights on the translation initiation complex: ghosts of a universal initiation complex
journal, February 2007
- Allen, Gregory S.; Frank, Joachim
- Molecular Microbiology, Vol. 63, Issue 4
The ribosome triggers the stringent response by RelA via a highly distorted tRNA
journal, July 2013
- Agirrezabala, Xabier; Fernández, Israel S.; Kelley, Ann C.
- EMBO reports, Vol. 14, Issue 9
Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding
journal, May 2011
- Dunkle, J. A.; Wang, L.; Feldman, M. B.
- Science, Vol. 332, Issue 6032
The structure of LepA, the ribosomal back translocase
journal, March 2008
- Evans, R. N.; Blaha, G.; Bailey, S.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 12
PHENIX : building new software for automated crystallographic structure determination
journal, October 2002
- Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei
- Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11
Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form
journal, November 2002
- Ogle, James M.; Murphy, Frank V.; Tarry, Michael J.
- Cell, Vol. 111, Issue 5
The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli
journal, November 2014
- Balakrishnan, Rohan; Oman, Kenji; Shoji, Shinichiro
- Nucleic Acids Research, Vol. 42, Issue 21
EF4 knockout E. coli cells exhibit lower levels of cellular biosynthesis under acidic stress
journal, April 2014
- Yang, Fang; Li, Zhikai; Hao, Jia
- Protein & Cell, Vol. 5, Issue 7
EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome
journal, January 2016
- Zhang, Dejiu; Yan, Kaige; Liu, Guangqiao
- Nature Structural & Molecular Biology, Vol. 23, Issue 2
Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome
journal, August 2014
- Gagnon, M. G.; Lin, J.; Bulkley, D.
- Science, Vol. 345, Issue 6197
Mechanical force releases nascent chain-mediated ribosome arrest in vitro and in vivo
journal, April 2015
- Goldman, D. H.; Kaiser, C. M.; Milin, A.
- Science, Vol. 348, Issue 6233
Translation factor LepA contributes to tellurite resistance in Escherichia coli but plays no apparent role in the fidelity of protein synthesis
journal, February 2010
- Shoji, Shinichiro; Janssen, Brian D.; Hayes, Christopher S.
- Biochimie, Vol. 92, Issue 2
Thiostrepton inhibits stable 70S ribosome binding and ribosome-dependent GTPase activation of elongation factor G and elongation factor 4
journal, September 2011
- Walter, Justin D.; Hunter, Margaret; Cobb, Melanie
- Nucleic Acids Research, Vol. 40, Issue 1
A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome
journal, August 2014
- Polikanov, Yury S.; Steitz, Thomas A.; Innis, C. Axel
- Nature Structural & Molecular Biology, Vol. 21, Issue 9
The crystal structure of unmodified tRNA Phe from Escherichia coli
journal, March 2010
- Byrne, Robert T.; Konevega, Andrey L.; Rodnina, Marina V.
- Nucleic Acids Research, Vol. 38, Issue 12
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation
journal, August 2008
- Connell, Sean R.; Topf, Maya; Qin, Yan
- Nature Structural & Molecular Biology, Vol. 15, Issue 9
Elongation factors on the ribosome
journal, June 2005
- Nilsson, Jakob; Nissen, Poul
- Current Opinion in Structural Biology, Vol. 15, Issue 3
Structure of the 70S Ribosome Complexed with mRNA and tRNA
journal, September 2006
- Selmer, M.
- Science, Vol. 313, Issue 5795
The Crystal Structure of the Ribosome Bound to EF-Tu and Aminoacyl-tRNA
journal, October 2009
- Schmeing, T. M.; Voorhees, R. M.; Kelley, A. C.
- Science, Vol. 326, Issue 5953
Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants
journal, December 1993
- Kabsch, W.
- Journal of Applied Crystallography, Vol. 26, Issue 6
Identification of Two Structural Elements Important for Ribosome-Dependent GTPase Activity of Elongation Factor 4 (EF4/LepA)
journal, February 2015
- De Laurentiis, Evelina Ines; Wieden, Hans-Joachim
- Scientific Reports, Vol. 5, Issue 1
Ribosome engineering to promote new crystal forms
journal, April 2012
- Selmer, Maria; Gao, Yong-Gui; Weixlbaumer, Albert
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 5
Effect of variation of charged and uncharged tRNA(Trp) levels on ppGpp synthesis in Escherichia coli.
journal, January 1989
- Rojiani, M. V.; Jakubowski, H.; Goldman, E.
- Journal of Bacteriology, Vol. 171, Issue 12
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Structural Basis of the Translational Elongation Cycle
journal, June 2013
- Voorhees, Rebecca M.; Ramakrishnan, V.
- Annual Review of Biochemistry, Vol. 82, Issue 1
Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation
journal, January 2015
- Lin, Jinzhong; Gagnon, Matthieu G.; Bulkley, David
- Cell, Vol. 160, Issue 1-2
Synthesis of Guanosine Tetra- and Pentaphosphate Requires the Presence of a Codon-Specific, Uncharged Transfer Ribonucleic Acid in the Acceptor Site of Ribosomes
journal, May 1973
- Haseltine, W. A.; Block, R.
- Proceedings of the National Academy of Sciences, Vol. 70, Issue 5, p. 1564-1568
The Highly Conserved LepA Is a Ribosomal Elongation Factor that Back-Translocates the Ribosome
journal, November 2006
- Qin, Yan; Polacek, Norbert; Vesper, Oliver
- Cell, Vol. 127, Issue 4
MSI and MSII made on Ribosome in Idling Step of Protein Synthesis
journal, August 1972
- Haseltine, William A.; Block, Ricardo; Gilbert, Walter
- Nature, Vol. 238, Issue 5364
Works referencing / citing this record:
Structural basis for ribosome recycling by RRF and tRNA
journal, December 2019
- Zhou, Dejian; Tanzawa, Takehito; Lin, Jinzhong
- Nature Structural & Molecular Biology, Vol. 27, Issue 1
Conserved GTPase LepA (Elongation Factor 4) functions in biogenesis of the 30S subunit of the 70S ribosome
journal, January 2017
- Gibbs, Michelle R.; Moon, Kyung-Mee; Chen, Menglin
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 5
Translation Elongation Factor 4 (LepA) Contributes to Tetracycline Susceptibility by Stalling Elongating Ribosomes
journal, May 2018
- Liu, Bin; Chen, Chunlai
- Antimicrobial Agents and Chemotherapy, Vol. 62, Issue 8
Ribosome Structure, Function, and Early Evolution
journal, December 2018
- Opron, Kristopher; Burton, Zachary
- International Journal of Molecular Sciences, Vol. 20, Issue 1
Similarity and diversity of translational GTPase factors EF-G, EF4, and BipA: From structure to function
journal, November 2016
- Ero, Rya; Kumar, Veerendra; Chen, Yun
- RNA Biology, Vol. 13, Issue 12
Retraction for Liu and Chen, “Translation Elongation Factor 4 (LepA) Contributes to Tetracycline Susceptibility by Stalling Elongating Ribosomes”
journal, February 2019
- Liu, Bin; Chen, Chunlai
- Antimicrobial Agents and Chemotherapy, Vol. 63, Issue 2
Ribosome Structure, Function, and Early Evolution
journal, December 2018
- Opron, Kristopher; Burton, Zachary
- International Journal of Molecular Sciences, Vol. 20, Issue 1