The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole

Journal of Molecular Biology

Volumn 367, Issue 5, 2007, Pages 1471-1479

  Schroeder, Susan J ^a   Blaha, Gregor ^a,b   Tirado Rives, Julian ^a   Steitz, Thomas A ^a,b   Moore, Peter B ^a  

^a YALE UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

13 deoxytedanolide; 50 S; E site; girodazole; ribosome

Indexed keywords

13 DEOXYTEDANOLIDE; ANTIBIOTIC AGENT; GIROLLINE; RIBOSOME PROTEIN; TRANSFER RNA; UNCLASSIFIED DRUG;

50S RIBOSOME SUBUNIT; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DRUG BINDING SITE; DRUG PROTEIN BINDING; DRUG SPECIFICITY; DRUG STRUCTURE; HALOARCULA MARISMORTUI; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS; PROTEIN SYNTHESIS REGULATION; RIBOSOME SUBUNIT; RNA BINDING;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; HALOARCULA MARISMORTUI;

EID: 33947096837     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.01.081     Document Type: Article

References (37)

1. Brodersen D.E., Clemons W.M., Carter A.P., Morgan-Warren R.J., Wimberly B.T., and Ramakrishnan V. The structural basis for the action of the antibiotics tetracycline, pactamycin and hygromycin B on the 30S subunit. Cell 103 (2000) 1143-1154
2. Carter A.P., Clemons W.M., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., and Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407 (2000) 340-348
3. Pioletti M., Schlunzen F., Harms J., Zarivach R., Glumann M., Avila H., et al. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J. 20 (2001) 1829-1839
4. Schluenzen F., Zarivach R., Harms J., Bashan A., Tocilj A., Albrecht R., et al. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413 (2001) 814-821
5. Hansen J.L., Ban N., Nissen P., Moore P.B., and Steitz T.A. The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol. Cell 10 (2002) 117-126
6. Auerbach T., Bashan A., Harms J., Schluenzen F., Zarivach R., Bartels H., et al. Antibiotics targeting ribosomes: crystallographic studies. Curr. Drug Targ. Infect. Disord. 2 (2002) 169-186
7. Berisio R., Harms J., Schluenzen F., Zarivach R., Hansen H.A.S., Fucini P., and Yonath A. Structural insight into the antibiotic action of telithromycin against resistant mutants. J. Bacteriol. 185 (2003) 4276-4279
8. Hansen J.L., Moore P.B., and Steitz T.A. Structure of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J. Mol. Biol. 330 (2003) 1061-1075
9. Harms J.M., Bartels H., Schluenzen F., and Yonath A. Antibiotics acting on the translational machinery. J. Cell Sci. 116 (2003) 1391-1393
10. Schluenzen F., Harms J.M., Franceschi F., Hansen H.A.S., Bartels H., Zarivach R., and Yonath A. Structural basis for the antibiotic activity of ketolides and azalides. Structure 11 (2003) 329-338
11. Harms J.M., Schluenzen F., Fucini P., Bartels H., and Yonath A. Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin. BMC Biol. 2 (2004) 4
12. Schluenzen F., Pyetan E., Fucini P., Yonath A., and Harms J.M. Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin. Mol. Microbiol. 54 (2004) 1287-1295
13. Tu D., Blaha G., Moore P.B., and Steitz T.A. Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 121 (2005) 257-270
14. Wilson D.N., Harms J.M., Nierhaus K.H., Schlunzen F., and Fucini P. Species-specific antibiotic-ribosome interactions: implications for drug development. Biol. Chem. 386 (2005) 1239-1252
15. Nishimura S., Matsunaga S., Yoshida M., Hirota H., Yokoyama S., and Fusetani N. 13-Deoxytedanolide, a marine sponge-derived antitumor macrolide, binds to the 60S large ribosomal subunit. Bioorgan. Med. Chem. 13 (2005) 449-454
16. Schmitz F.J., Gunasekera S.P., Yalamanchili G., Hossain M.B., and van der Helm D. Tedanolide: a potent cytotoxic macrolide from the Caribbean sponge Tedania ignis. J. Am. Chem. Soc. 106 (1984) 7251-7252
17. Fusetani N., Sugawara T., Matsunaga S., and Hirota H. Cytotoxic metabolites of the marine sponge Mycale adhaerans Lambe. J. Org. Chem. 56 (1991) 4971-4974
18. Ahond A., Bedoya Z.M., Colin M., Fizames C., Laboute P., Lavelle F., et al. La giroline, nouvelle substance antitumorale extraite de l'eponge Pseudaxinyssa cantharella. C.R. Acad. Sci. Paris 307 (1988) 145-148
19. Lavelle F., Zerial A., Dizames C., Rabault B., and Curaudeau A. Antitumor activity and mechanism of action of the marine compound girodazole. Investigat. New Drugs 9 (1991) 233-244
20. Colson G., Rabault B., Lavelle F., and Zerial A. Mode of action of the antitumor compound girodazole (RP 49532A, NSC 627434). Biochem. Pharmacol. 43 (1992) 1717-1723
21. Jorgensen W.L., and Tirado-Rives J. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J. Comput. Chem. 26 (2005) 1689-1700
22. Jorgensen W.L., and Tirado-Rives J. Chemical theory and computation special feature: potential energy function for atomic-level simulation of water and organic and biomolecular systems. Proc. Natl Acad. Sci. USA 102 (2005) 6665-6670
23. Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., et al. The comparative RNA web (CRW) site: an outline database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BioMed Centr. Bioinform. 3 (2002) 2
24. Schmeing T.M., Moore P.B., and Steitz T.A. Structure of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. RNA 9 (2003) 1345-1352
25. Selmer M., Dunham C.M., Murphy F.V.I., Weixibaumer A., Petry S., Kelley A.C., et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942
26. Korostelev A., Trakhanov S., Laurberg M., and Noller H.F. Crystal structure of a 70S ribosome-tRNA complex reveals functional interations and rearrangements. Cell 126 (2006) 1065-1077
27. Nishimura S., Matsunaga S., Yoshida S., Nakao Y., Hirota H., and Fusetani N. Structure-activity relationship study on 13-deoxytedanolide, a highly antitumor macrolide from the marine sponge Mycale adhaerens. Bioorgan. Med. Chem. 13 (2005) 455-462
28. Kawai S., Mirato S., Mochizuki M., Shibaya I., Yano K., and Tagaki M. Drastic alteration of cycloheximide sensitivity by substitution of one amino acid in the L41 ribosomal protein of yeast. J. Bacteriol. 174 (1992) 254-262
29. Pestova T.V., and Hellen C.U.T. Translation elongation after assembly of ribosomes on the cricket paralysis virus internal ribosome entry site without initiation factor or initiator tRNA. Gen. Dev. 17 (2003) 181-186
30. Cooper D., Banthorpe D.V., and Wilkie D. Modified ribosomes conferring resistance to cylcloheximide in mutants of Saccharomyces cerevisiae. J. Mol. Biol. 26 (1967) 347-350
31. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., VCila-Sanjuro A., Holton J.H., and Doudna Cate J.H. Structure of the bacterial ribosome at 3.5 Å resolution. Science 310 (2005) 827-834
32. Ban N., Nissen P., Hansen J., Moore P.B., and Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289 (2000) 905-920
33. Schmeing T.M., Huang K.S., Strobel S.A., and Steitz T.A. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438 (2005) 520-524
34. Klein D.J., Moore P.B., and Steitz T.A. The roles of ribosomal proteins in the structure, assemby and evolution of the large ribosomal subunit. J. Mol. Biol. 340 (2004) 141-177
35. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system (CNS): a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
36. Schuettelkopf A.W., and van Aalten D.M.F. PRODRG: a tool for high-throughput crystallography of protein ligand complexes. Acta Crystallog. sect. D 60 (2004) 1355-1363
37. Jones T.A., Cowan S., Zou J.-Y., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 46 (1991) 110-119