The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome

Viomycin and capreomycin belong to the tuberactinomycin family of antibiotics, which are among the most effective antibiotics against multidrug-resistant tuberculosis. Here we present two crystal structures of the 70S ribosome in complex with three tRNAs and bound to either viomycin or capreomycin at 3.3- and 3.5-Å resolution, respectively. Both antibiotics bind to the same site on the ribosome, which lies at the interface between helix 44 of the small ribosomal subunit and helix 69 of the large ribosomal subunit. The structures of these complexes suggest that the tuberactinomycins inhibit translocation by stabilizing the tRNA in the A site in the pretranslocation state. In addition, these structures show that the tuberactinomycins bind adjacent to the binding sites for the paromomycin and hygromycin B antibiotics, which may enable the development of new derivatives of tuberactinomycins that are effective against drug-resistant strains.

[1]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[2]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[3]  Earl B. Herr,et al.  CHEMICAL AND PHYSICAL CHARACTERIZATION OF CAPREOMYCIN , 1966, Annals of the New York Academy of Sciences.

[4]  C. Dolea,et al.  World Health Organization , 1949, International Organization.

[5]  Daniel N. Wilson,et al.  New features of the ribosome and ribosomal inhibitors: non-enzymatic recycling, misreading and back-translocation. , 2008, Journal of molecular biology.

[6]  G. Langlet,et al.  International Tables for Crystallography , 2002 .

[7]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[8]  J. Holton,et al.  Structures of the Bacterial Ribosome at 3.5 Å Resolution , 2005, Science.

[9]  J. Cate,et al.  Structures of the Ribosome in Intermediate States of Ratcheting , 2009, Science.

[10]  V. Ramakrishnan,et al.  Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit , 2001, Science.

[11]  B. Cooperman,et al.  Kinetically competent intermediates in the translocation step of protein synthesis. , 2007, Molecular cell.

[12]  Stewart T. Cole,et al.  Benzothiazinones Kill Mycobacterium tuberculosis by Blocking Arabinan Synthesis , 2009, Science.

[13]  H. Noller,et al.  Structural basis for translation termination on the 70S ribosome , 2008, Nature.

[14]  M. Selmer,et al.  Structure of the 70S Ribosome Complexed with mRNA and tRNA , 2006, Science.

[15]  Jianlin Lei,et al.  Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. , 2008, Molecular cell.

[16]  Christine Mayer,et al.  Conformational change of Escherichia coli initiator methionyl-tRNAfMet upon binding to methionyl-tRNA formyl transferase , 2002, Nucleic Acids Res..

[17]  M. O’Connor.  Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs , 2009, Molecular Genetics and Genomics.

[18]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[19]  V. Ramakrishnan,et al.  Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome , 2009, Nature Structural &Molecular Biology.

[20]  S. Douthwaite,et al.  Capreomycin binds across the ribosomal subunit interface using tlyA-encoded 2'-O-methylations in 16S and 23S rRNAs. , 2006, Molecular cell.

[21]  B. Bycroft.  The crystal structure of viomycin, a tuberculostatic antibiotic , 1972 .

[22]  J. Blanchard,et al.  Meropenem-Clavulanate Is Effective Against Extensively Drug-Resistant Mycobacterium tuberculosis , 2009, Science.

[23]  H. Noller,et al.  Deletion of a conserved, central ribosomal intersubunit RNA bridge. , 2006, Molecular cell.

[24]  Sarah E. Walker,et al.  Ribosomal translocation: one step closer to the molecular mechanism. , 2009, ACS chemical biology.

[25]  T. Noda,et al.  Chemical studies on tuberactinomycin. II. The structure of tuberactinomycin 0 , 1971 .

[26]  Y. Chan,et al.  Deciphering Tuberactinomycin Biosynthesis: Isolation, Sequencing, and Annotation of the Viomycin Biosynthetic Gene Cluster , 2003, Antimicrobial Agents and Chemotherapy.

[27]  A. Mallampalli,et al.  Review: Managing TB in the 21st century: existing and novel drug therapies , 2008, Therapeutic advances in respiratory disease.

[28]  Wolfgang Wintermeyer,et al.  Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation. , 2004, Journal of molecular biology.

[29]  J. Modolell,et al.  The inhibition of ribosomal translocation by viomycin. , 1977, European journal of biochemistry.

[30]  T. Yamada,et al.  Resistance to viomycin conferred by RNA of either ribosomal subunit , 1978, Nature.

[31]  V. Ramakrishnan,et al.  Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics , 2000, Nature.

[32]  Steven Chu,et al.  Fluctuations of transfer RNAs between classical and hybrid states. , 2007, Biophysical journal.

[33]  T. Shiba,et al.  Activity of Di-β-Lysyl-Capreomycin IIA and Palmitoyl Tuberactinamine N Against Drug-Resistant Mutants with Altered Ribosomes , 1981, Antimicrobial Agents and Chemotherapy.

[34]  A. Brunger.  Version 1.2 of the Crystallography and NMR system , 2007, Nature Protocols.

[35]  T. Steitz,et al.  Overproduction and purification of Escherichia coli tRNA(2Gln) and its use in crystallization of the glutaminyl-tRNA synthetase-tRNA(Gln) complex. , 1988, Journal of molecular biology.

[36]  J. Holton,et al.  Structural basis for aminoglycoside inhibition of bacterial ribosome recycling , 2007, Nature Structural &Molecular Biology.

[37]  Zigurts K. Majumdar,et al.  The antibiotic viomycin traps the ribosome in an intermediate state of translocation , 2007, Nature Structural &Molecular Biology.

[38]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[39]  J. Cate,et al.  Structural basis for hygromycin B inhibition of protein biosynthesis. , 2008, RNA.

[40]  M. Selmer,et al.  Crystal structure of the ribosome recycling factor bound to the ribosome , 2007, Nature Structural &Molecular Biology.

[41]  Federico D. Sacerdoti,et al.  Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters , 2006, ACM/IEEE SC 2006 Conference (SC'06).

[42]  Sabine Petry,et al.  Insights into Translational Termination from the Structure of RF2 Bound to the Ribosome , 2008, Science.

[43]  Scott M Stagg,et al.  Modeling a minimal ribosome based on comparative sequence analysis. , 2002, Journal of molecular biology.

[44]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[45]  T. Martin Schmeing,et al.  An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA , 2005, Nature.

[46]  Stefan Weigand,et al.  Antibacterial natural products in medicinal chemistry--exodus or revival? , 2006, Angewandte Chemie.

[47]  T. Steitz,et al.  Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70S Ribosome , 2009, Science.

[48]  Taekjip Ha,et al.  Spontaneous intersubunit rotation in single ribosomes. , 2008, Molecular cell.

[49]  S. Sild,et al.  Ribosomal intersubunit bridge B2a is involved in factor-dependent translation initiation and translational processivity. , 2009, Journal of molecular biology.

[50]  T. Shiba,et al.  Chemical studies on tuberactinomycin. XIII. Modification of beta-ureidodehydroalanine residue in tuberactinomycin N. , 1977, The Journal of antibiotics.

[51]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[52]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[53]  T. Noda,et al.  CHEMICAL STUDIES ON TUBERACTINOMYCIN. III , 1972 .

[54]  Jianyu Zhu,et al.  Crystal structure of a translation termination complex formed with release factor RF2 , 2008, Proceedings of the National Academy of Sciences.

[55]  Harry F. Noller,et al.  Intermediate states in the movement of transfer RNA in the ribosome , 1989, Nature.

[56]  M. Rodnina,et al.  Colicin E3 cleavage of 16S rRNA impairs decoding and accelerates tRNA translocation on Escherichia coli ribosomes , 2008, Molecular microbiology.

[57]  S. Douthwaite,et al.  Mutations in Conserved Helix 69 of 23S rRNA of Thermus thermophilus That Affect Capreomycin Resistance but Not Posttranscriptional Modifications , 2008, Journal of bacteriology.