56
|
Valle M, Sengupta J, Swami NK, Grassucci RA, Burkhardt N, Nierhaus KH, Agrawal RK, Frank J. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J 2002; 21:3557-67. [PMID: 12093756 PMCID: PMC126079 DOI: 10.1093/emboj/cdf326] [Citation(s) in RCA: 252] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon-anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition.
Collapse
MESH Headings
- Anticodon/genetics
- Codon/genetics
- Cryoelectron Microscopy
- Escherichia coli/chemistry
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/ultrastructure
- Guanosine Diphosphate/chemistry
- Guanosine Triphosphate/metabolism
- Image Processing, Computer-Assisted
- Macromolecular Substances
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/ultrastructure
- Protein Conformation
- Pyridones/pharmacology
- RNA, Transfer/chemistry
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Amino Acyl/physiology
- RNA, Transfer, Amino Acyl/ultrastructure
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Ribosomes/chemistry
- Ribosomes/drug effects
- Ribosomes/ultrastructure
- Structure-Activity Relationship
Collapse
Affiliation(s)
- Mikel Valle
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Jayati Sengupta
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Neil K. Swami
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Robert A. Grassucci
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Nils Burkhardt
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Knud H. Nierhaus
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Rajendra K. Agrawal
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Joachim Frank
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| |
Collapse
|
64
|
Pioletti M, Schlünzen F, Harms J, Zarivach R, Glühmann M, Avila H, Bashan A, Bartels H, Auerbach T, Jacobi C, Hartsch T, Yonath A, Franceschi F. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J 2001; 20:1829-39. [PMID: 11296217 PMCID: PMC125237 DOI: 10.1093/emboj/20.8.1829] [Citation(s) in RCA: 362] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit.
Collapse
Affiliation(s)
- Marta Pioletti
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Frank Schlünzen
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Jörg Harms
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Raz Zarivach
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Marco Glühmann
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Horacio Avila
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Anat Bashan
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Heike Bartels
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Tamar Auerbach
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Carsten Jacobi
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Thomas Hartsch
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - Ada Yonath
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| | - François Franceschi
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, FB Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Max-Planck-Research Unit for Ribosomal Structure, Notkestrasse 85, 22603 Hamburg, Göttingen Genomics Laboratory, Georg-August Universität, Griesebacherstrasse 8, 37077 Göttingen, Germany, Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel and Centro de Investigaciones Biomédicas, Universidad de Carabobo, Las Delicias, Maracay, Venezuela Corresponding author e-mail:
M.Pioletti, F.Schlünzen and J.Harms contributed equally to this work
| |
Collapse
|