Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression (465 views)
Mol Cell (ISSN: 1097-2765, 1097-4164), 2003 Jan; 11(1): 91-102.
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Paper type: Journal Article,
Impact factor: 16.835, 5-year impact factor: 15.324
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-0037249473&partnerID=40&md5=52d8a5e881217cbef1352eca066e6a15
Keywords: Peptidyltransferase, Puromycin, Ribosome Rna, Transfer Rna, Article, Chemical Bond, Chemical Interaction, Conformational Transition, Crystal Structure, Deinococcus Radiodurans, Nonhuman, Protein Conformation, Ribosome Subunit, Rna Structure, Rna Transport, Bacterial Proteins, Catalytic Domain, Crystallography, X-Ray, Models, Molecular, Molecular Structure, Nucleic Acid Conformation, Protein Biosynthesis, Protein Synthesis Inhibitors, Ribosomal Proteins, Amino Acyl, Sparsomycin,
Affiliations:
*** IBB - CNR ***
Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel
Max-Planck-Res. U. for Ribosomal S., Notkestrasse 85, 22603 Hamburg, Germany
FB Biologie, Chemie, Pharmazie, Frei University Berlin, Takustrasse 3, 14195 Berlin, Germany
Inst. of Biostructures and Bioimages, CNR, 80138 Napoli, Italy
References:
Bailey, S., The CCP4 suite: Programs for protein crystallography (1994) Acta Crystallogr. D, 50, pp. 760-76
Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A., The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution (2000) Science, 289, pp. 905-920
Barta, A., Dorner, S., Polacek, N., Mechanism of ribosomal peptide bond formation (2001) Science, 291, p. 203
Bayfield, M.A., Dahlberg, A.E., Schulmeister, U., Dorner, S., Barta, A., A conformational change in the ribosomal peptidyltransferase center upon active/inactive transition (2001) Proc. Natl. Acad. Sci. USA, 98, pp. 10096-10101
Bourd, S.B., Kukhanova, M.K., Gottikh, B.P., Krayevsky, A.A., Cooperative effects in the peptidyltransferase center of Escherichia coli ribosomes (1983) Eur. J. Biochem., 135, pp. 465-470
Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Pannu, N.S., Crystallography & NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallogr. D Biol. Crystrallogr., 54, pp. 905-921
Cooperman, B.S., Identification of binding sites on the E. coli ribosome by affinity labeling, Adv (1977) Exp. Med. Biol., 86 A, pp. 595-609
Cundliffe, E., (1981) Antibiotic Inhibitors of Ribosome Function, , E.F. Gale, E. Cundliffe, P.E. Reynolds, M.H. Richmond, and M. H. Waring, eds. (London, NY, Sydney, Toronto: Wiley)
Cundliffe, E., Recognition sites for antibiotics within rRNA (1990) The Ribosome: Structure, , W.E. Function and Evolution, A.E. Hill, R.A. Dahlberg, P.B. Garrett, D. Moore, Schlessinger, & J.R. Warner. Washington, DC: ASM. 479-90.pp
Eckerman, D.J., Symons, R.H., Sequence at the site of attachment of an affinity-label derivative of puromycin on 23S ribosomal RNA of E. coli ribosomes (1978) Eur. J. Biochem., 82, pp. 225-234
Frank, J., Agrawal, R.K., A ratchet-like inter-subunit reorganization of the ribosome during translocation (2000) Nature, 406, pp. 318-322
Gale, E.F., Cundliffe, E., Reynolds, P.E., Richmond, M.H., Waring, M.J., (1981) The Molecular Basis of Antibiotic Action, , London: Wiley
Garrett, R.A., Rodriguez-Fonseca, C., The peptidyltransferase center (1995) Ribosomal RNA: Structure, , Processing Evolution, R.A. Function, A.E. Zimmermann and, & Dahlberg. Boca Raton: CRC Press. 327-355.pp
Goldberg, I.H., Mitsugi, K., Sparsomycin, an inhibitor of aminoacyl transfer to polypeptide (1966) Biochem. Biophys. Res. Commun., 23, pp. 453-459
Green, R., Samaha, R.R., Noller, H.F., Mutations at nucleotides G2251 and U2585 of 23S rRNA perturb the peptidyltransferase center of the ribosome (1997) J. Mol. Biol., 266, pp. 40-50
Green, R., Switzer, C., Noller, H.F., Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA (1998) Science, 280, pp. 286-289
Gutell, R.R., Gray, M.W., Schnare, M.N., A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993 (1993) Nucleic Acids Res., 21, pp. 3055-3074
Hall, C.C., Johnson, D., Cooperman, B.S., [3H]-p-azidopuromycin photoaffinity labeling of E. coli ribosomes: Evidence for site-specific interaction at U-2504 and G-2502 in domain V of 23S ribosomal RNA (1988) Biochemistry, 27, pp. 3983-3990
Hansen, J.L., Schmeing, T.M., Moore, P.B., Steitz, T.A., Structural insights into peptide bond formation (2002) Proc. Natl. Acad. Sci. USA, 99, pp. 1670-1675
Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Yonath, A., High-resolution structure of the large ribosomal subunit from a mesophilic eubacterium (2001) Cell, 107, pp. 679-688
Hornig, H., Woolley, P., Luhrmann, R., Decoding at the ribosomal A site: Antibiotics, misreading and energy of aminoacyl-tRNA binding (1987) Biochimie, 69, pp. 803-813
Hummel, H., Bock, A., 23S ribosomal RNA mutations in halobacteria conferring resistance to the anti-80S ribosome targeted antibiotic anisomycin (1987) Nucleic Acids Res., 15, pp. 2431-2443
Kim, D.F., Green, R., Base-pairing between 23S rRNA and tRNA in the ribosomal A site (1999) Mol. Cell, 4, pp. 859-864
Kirillov, S., Porse, B.T., Vester, B., Woolley, P., Garrett, R.A., Movement of the 3′-end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics (1997) FEBS Lett., 406, pp. 223-233
Kirillov, S.V., Porse, B.T., Garrett, R.A., Peptidyltransferase antibiotics perturb the relative positioning of the 3′-terminal adenosine of P/P'-site-bound tRNA and 23S rRNA in the ribosome (1999) RNA, 5, pp. 1003-1013
Lazaro, E., Van den Broek, L.A., San Felix, A., Ottenheijm, H.C., Ballesta, J.P., Biochemical and kinetic characteristics of the interaction of the antitumor antibiotic sparsomycin with prokaryotic and eukaryotic ribosomes (1991) Biochemistry, 30, pp. 9642-9648
Lazaro, E., Rodriguez-Fonseca, C., Porse, B., Urena, D., Garrett, R.A., Ballesta, J.P., A sparsomycin-resistant mutant of Halobacterium salinarium lacks a modification at nucleotide U2603 in the peptidyl transferase centre of 23S RNA (1996) J. Mol. Biol., 261, pp. 231-238
Lill, R., Wintermeyer, W., Destabilization of codon-anticodon interaction in the ribosomal exit site (1987) J. Mol. Biol., 196, pp. 137-148
Mankin, A.S., Garrett, R.A., Chloramphenicol resistance mutations in the single 23S rRNA gene of the archaeon H. halobium (1991) J. Bacteriol., 173, pp. 3559-3563
Miskin, R., Zamir, A., Elson, D., The inactivation and reactivation of ribosomal-peptidyltransferase of E. coli (1968) Biochem. Biophys. Res. Commun., 33, pp. 551-557
Moazed, D., Noller, H.F., Intermediate states in the movement of transfer RNA in the ribosome (1989) Nature, 342, pp. 142-148
Monro, R.E., Cerna, J., Marcker, K.A., Ribosome-catalyzed peptidyl transfer: Substrate specificity at the P-site (1968) Proc. Natl. Acad. Sci. USA, 61, pp. 1042-1049
Monro, R.E., Celma, M.L., Vazquez, D., Action of sparsomycin on ribosome-catalysed peptidyl transfer (1969) Nature, 222, pp. 356-358
Nierhaus, K.H., Schulze, H., Cooperman, B.S., Molecular mechanisms of the ribosomal peptidyl transferase center (1980) Biochem. Int., 1, pp. 185-192
Noller, H.F., Hoffarth, V., Zimniak, L., Unusual resistance of peptidyltransferase to protein extraction procedures (1992) Science, 256, pp. 1416-1419
Noller, H.F., Yusupov, M.M., Yusupova, G.Z., Baucom, A., Cate, J.H.D., Translocation of tRNA during protein synthesis (2002) FEBS Lett., 514, pp. 11-16
Odom, O.W., Picking, W.D., Hardesty, B., Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes (1990) Biochemistry, 29, pp. 10734-10744
Ofengand, J., Bakin, A., Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria, and chloroplasts (1997) J. Mol Biol., 266, pp. 246-268
Otwinowski, Z., Minor, W., Processing of X-ray diffraction data collected in oscillation mode (1997) Macromolecular Crystallogr. Pt A, 276, pp. 307-326
Pape, T., Wintermeyer, W., Rodnina, M., Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome (1999) EMBO J., 18, pp. 3800-3807
Pestka, S., Inhibitors of protein synthesis (1977) Molecular Mechanisms of Protein Biosynthesis, , H. Weissbach, & S. Pestka. New York: Academic Press. 467-553.pp
Polacek, N., Gaynor, M., Yassin, A., Mankin, A.S., Ribosomal peptidyltransferase can withstand mutations at the putative catalytic nucleotide (2001) Nature, 411, pp. 498-501
Porse, B.T., Kirillov, S.V., Awayez, M.J., Ottenheijm, H.C., Garrett, R.A., Direct crosslinking of the antitumor antibiotic sparsomycin, and its derivatives, to A2602 in the peptidyltransferase center of 23S-like rRNA within ribosome-tRNA complexes (1999) Proc. Natl. Acad. Sci. USA, 96, pp. 9003-9008
Rheinberger, H.J., Sternbach, H., Nierhaus, K.H., Three tRNA binding sites on Escherichia coli ribosomes (1981) Proc. Natl. Acad. Sci. USA, 78, pp. 5310-5314
Samaha, R.R., Green, R., Noller, H.F., A base pair between tRNA and 23S rRNA in the peptidyltransferase centre of the ribosome (1995) Nature, 377, pp. 309-314
Schmeing, T.M., Seila, A.C., Hansen, J.L., Freeborn, B., Soukup, J.K., Scaringe, S.A., Strobel, S.A., Steitz, T.A., A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits (2002) Nat. Struct. Biol., 9, pp. 225-230
Shevack, A., Gewitz, H.S., Hennemann, B., Yonath, A., Wittmann, H.G., Characterization and crystallization of ribosomal particles from Halobacterium marismortui (1985) FEBS Lett., 184, pp. 68-71
Smith, J.D., Traut, R.R., Blackburn, G.M., Monro, R.E., Action of puromycin in polyadenylic acid-directed polylysine synthesis (1965) J. Mol. Biol., 13, pp. 617-628
Stark, H., Orlova, E.V., Rinke-Appel, J., Junke, N., Mueller, F., Rodnina, M., Wintermeyer, W., Van Heel, M., Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy (1997) Cell, 88, pp. 19-28
Tan, G.T., DeBlasio, A., Mankin, A.S., Mutations in the peptidyltransferase center of 23S rRNA reveal the site of action of sparsomycin, a universal inhibitor of translation (1996) J. Mol. Biol., 261, pp. 222-230
Theocharis, D.A., Coutsogeorgopoulos, C., Mechanism of action of sparsomycin in protein synthesis (1992) Biochemistry, 31, pp. 5861-5868
Thompson, J., Kim, D.F., O'Connor, M., Lieberman, K.R., Bayfield, M.A., Gregory, S.T., Green, R., Dahlberg, A.E., Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit (2001) Proc. Natl. Acad. Sci. USA, 98, pp. 9002-9007
Traut, R.R., Monro, R.E., The puromycin reaction and its relationship to protein synthesis (1964) J. Mol. Biol., 10, pp. 63-72
Vazquez, D., Inhibitors of protein biosynthesis (1979) Mol. Biol. Biochem. Biophys., 30, pp. 1-312
Vester, B., Garrett, R.A., The importance of highly conserved nucleotides in the binding region of chloramphenicol at the peptidyltransfer center of E. coli 23S ribosomal RNA (1988) EMBO J., 7, pp. 3577-3588
Wilson, K.S., Noller, H.F., Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing (1998) Cell, 92, pp. 131-139
Yonath, A., The search and its outcome (2002) Annu. Rev. Biophys. Biomol. Struct., 31, pp. 257-273
Bayfield, M. A., Dahlberg, A. E., Schulmeister, U., Dorner, S., Barta, A., A conformational change in the ribosomal peptidyltransferase center upon active/inactive transition (2001) Proc. Natl. Acad. Sci. USA, 98, pp. 10096-10101
Bourd, S. B., Kukhanova, M. K., Gottikh, B. P., Krayevsky, A. A., Cooperative effects in the peptidyltransferase center of Escherichia coli ribosomes (1983) Eur. J. Biochem., 135, pp. 465-470
Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Pannu, N. S., Crystallography & NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallogr. D Biol. Crystrallogr., 54, pp. 905-921
Cooperman, B. S., Identification of binding sites on the E. coli ribosome by affinity labeling, Adv (1977) Exp. Med. Biol., 86 A, pp. 595-609
Eckerman, D. J., Symons, R. H., Sequence at the site of attachment of an affinity-label derivative of puromycin on 23S ribosomal RNA of E. coli ribosomes (1978) Eur. J. Biochem., 82, pp. 225-234
Gale, E. F., Cundliffe, E., Reynolds, P. E., Richmond, M. H., Waring, M. J., (1981) The Molecular Basis of Antibiotic Action, , London: Wiley
Garrett, R. A., Rodriguez-Fonseca, C., The peptidyltransferase center (1995) Ribosomal RNA: Structure, , Processing Evolution, R. A. Function, A. E. Zimmermann and, & Dahlberg. Boca Raton: CRC Press. 327-355. pp
Goldberg, I. H., Mitsugi, K., Sparsomycin, an inhibitor of aminoacyl transfer to polypeptide (1966) Biochem. Biophys. Res. Commun., 23, pp. 453-459
Gutell, R. R., Gray, M. W., Schnare, M. N., A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993 (1993) Nucleic Acids Res., 21, pp. 3055-3074
Hall, C. C., Johnson, D., Cooperman, B. S., [3H] -p-azidopuromycin photoaffinity labeling of E. coli ribosomes: Evidence for site-specific interaction at U-2504 and G-2502 in domain V of 23S ribosomal RNA (1988) Biochemistry, 27, pp. 3983-3990
Hansen, J. L., Schmeing, T. M., Moore, P. B., Steitz, T. A., Structural insights into peptide bond formation (2002) Proc. Natl. Acad. Sci. USA, 99, pp. 1670-1675
Kim, D. F., Green, R., Base-pairing between 23S rRNA and tRNA in the ribosomal A site (1999) Mol. Cell, 4, pp. 859-864
Kirillov, S. V., Porse, B. T., Garrett, R. A., Peptidyltransferase antibiotics perturb the relative positioning of the 3 -terminal adenosine of P/P'-site-bound tRNA and 23S rRNA in the ribosome (1999) RNA, 5, pp. 1003-1013
Mankin, A. S., Garrett, R. A., Chloramphenicol resistance mutations in the single 23S rRNA gene of the archaeon H. halobium (1991) J. Bacteriol., 173, pp. 3559-3563
Monro, R. E., Cerna, J., Marcker, K. A., Ribosome-catalyzed peptidyl transfer: Substrate specificity at the P-site (1968) Proc. Natl. Acad. Sci. USA, 61, pp. 1042-1049
Monro, R. E., Celma, M. L., Vazquez, D., Action of sparsomycin on ribosome-catalysed peptidyl transfer (1969) Nature, 222, pp. 356-358
Nierhaus, K. H., Schulze, H., Cooperman, B. S., Molecular mechanisms of the ribosomal peptidyl transferase center (1980) Biochem. Int., 1, pp. 185-192
Noller, H. F., Hoffarth, V., Zimniak, L., Unusual resistance of peptidyltransferase to protein extraction procedures (1992) Science, 256, pp. 1416-1419
Noller, H. F., Yusupov, M. M., Yusupova, G. Z., Baucom, A., Cate, J. H. D., Translocation of tRNA during protein synthesis (2002) FEBS Lett., 514, pp. 11-16
Odom, O. W., Picking, W. D., Hardesty, B., Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes (1990) Biochemistry, 29, pp. 10734-10744
Porse, B. T., Kirillov, S. V., Awayez, M. J., Ottenheijm, H. C., Garrett, R. A., Direct crosslinking of the antitumor antibiotic sparsomycin, and its derivatives, to A2602 in the peptidyltransferase center of 23S-like rRNA within ribosome-tRNA complexes (1999) Proc. Natl. Acad. Sci. USA, 96, pp. 9003-9008
Rheinberger, H. J., Sternbach, H., Nierhaus, K. H., Three tRNA binding sites on Escherichia coli ribosomes (1981) Proc. Natl. Acad. Sci. USA, 78, pp. 5310-5314
Samaha, R. R., Green, R., Noller, H. F., A base pair between tRNA and 23S rRNA in the peptidyltransferase centre of the ribosome (1995) Nature, 377, pp. 309-314
Schmeing, T. M., Seila, A. C., Hansen, J. L., Freeborn, B., Soukup, J. K., Scaringe, S. A., Strobel, S. A., Steitz, T. A., A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits (2002) Nat. Struct. Biol., 9, pp. 225-230
Smith, J. D., Traut, R. R., Blackburn, G. M., Monro, R. E., Action of puromycin in polyadenylic acid-directed polylysine synthesis (1965) J. Mol. Biol., 13, pp. 617-628
Tan, G. T., DeBlasio, A., Mankin, A. S., Mutations in the peptidyltransferase center of 23S rRNA reveal the site of action of sparsomycin, a universal inhibitor of translation (1996) J. Mol. Biol., 261, pp. 222-230
Theocharis, D. A., Coutsogeorgopoulos, C., Mechanism of action of sparsomycin in protein synthesis (1992) Biochemistry, 31, pp. 5861-5868
Traut, R. R., Monro, R. E., The puromycin reaction and its relationship to protein synthesis (1964) J. Mol. Biol., 10, pp. 63-72
Wilson, K. S., Noller, H. F., Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing (1998) Cell, 92, pp. 131-139
Mol Cell (ISSN: 1097-2765, 1097-4164), 2003 Jan; 11(1): 91-102.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 16.835, 5-year impact factor: 15.324
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-0037249473&partnerID=40&md5=52d8a5e881217cbef1352eca066e6a15
Keywords: Peptidyltransferase, Puromycin, Ribosome Rna, Transfer Rna, Article, Chemical Bond, Chemical Interaction, Conformational Transition, Crystal Structure, Deinococcus Radiodurans, Nonhuman, Protein Conformation, Ribosome Subunit, Rna Structure, Rna Transport, Bacterial Proteins, Catalytic Domain, Crystallography, X-Ray, Models, Molecular, Molecular Structure, Nucleic Acid Conformation, Protein Biosynthesis, Protein Synthesis Inhibitors, Ribosomal Proteins, Amino Acyl, Sparsomycin,
Affiliations:
*** IBB - CNR ***
Department of Structural Biology, Weizmann Institute, 76100 Rehovot, Israel
Max-Planck-Res. U. for Ribosomal S., Notkestrasse 85, 22603 Hamburg, Germany
FB Biologie, Chemie, Pharmazie, Frei University Berlin, Takustrasse 3, 14195 Berlin, Germany
Inst. of Biostructures and Bioimages, CNR, 80138 Napoli, Italy
References:
Bailey, S., The CCP4 suite: Programs for protein crystallography (1994) Acta Crystallogr. D, 50, pp. 760-76
Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A., The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution (2000) Science, 289, pp. 905-920
Barta, A., Dorner, S., Polacek, N., Mechanism of ribosomal peptide bond formation (2001) Science, 291, p. 203
Bayfield, M.A., Dahlberg, A.E., Schulmeister, U., Dorner, S., Barta, A., A conformational change in the ribosomal peptidyltransferase center upon active/inactive transition (2001) Proc. Natl. Acad. Sci. USA, 98, pp. 10096-10101
Bourd, S.B., Kukhanova, M.K., Gottikh, B.P., Krayevsky, A.A., Cooperative effects in the peptidyltransferase center of Escherichia coli ribosomes (1983) Eur. J. Biochem., 135, pp. 465-470
Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Pannu, N.S., Crystallography & NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallogr. D Biol. Crystrallogr., 54, pp. 905-921
Cooperman, B.S., Identification of binding sites on the E. coli ribosome by affinity labeling, Adv (1977) Exp. Med. Biol., 86 A, pp. 595-609
Cundliffe, E., (1981) Antibiotic Inhibitors of Ribosome Function, , E.F. Gale, E. Cundliffe, P.E. Reynolds, M.H. Richmond, and M. H. Waring, eds. (London, NY, Sydney, Toronto: Wiley)
Cundliffe, E., Recognition sites for antibiotics within rRNA (1990) The Ribosome: Structure, , W.E. Function and Evolution, A.E. Hill, R.A. Dahlberg, P.B. Garrett, D. Moore, Schlessinger, & J.R. Warner. Washington, DC: ASM. 479-90.pp
Eckerman, D.J., Symons, R.H., Sequence at the site of attachment of an affinity-label derivative of puromycin on 23S ribosomal RNA of E. coli ribosomes (1978) Eur. J. Biochem., 82, pp. 225-234
Frank, J., Agrawal, R.K., A ratchet-like inter-subunit reorganization of the ribosome during translocation (2000) Nature, 406, pp. 318-322
Gale, E.F., Cundliffe, E., Reynolds, P.E., Richmond, M.H., Waring, M.J., (1981) The Molecular Basis of Antibiotic Action, , London: Wiley
Garrett, R.A., Rodriguez-Fonseca, C., The peptidyltransferase center (1995) Ribosomal RNA: Structure, , Processing Evolution, R.A. Function, A.E. Zimmermann and, & Dahlberg. Boca Raton: CRC Press. 327-355.pp
Goldberg, I.H., Mitsugi, K., Sparsomycin, an inhibitor of aminoacyl transfer to polypeptide (1966) Biochem. Biophys. Res. Commun., 23, pp. 453-459
Green, R., Samaha, R.R., Noller, H.F., Mutations at nucleotides G2251 and U2585 of 23S rRNA perturb the peptidyltransferase center of the ribosome (1997) J. Mol. Biol., 266, pp. 40-50
Green, R., Switzer, C., Noller, H.F., Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA (1998) Science, 280, pp. 286-289
Gutell, R.R., Gray, M.W., Schnare, M.N., A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993 (1993) Nucleic Acids Res., 21, pp. 3055-3074
Hall, C.C., Johnson, D., Cooperman, B.S., [3H]-p-azidopuromycin photoaffinity labeling of E. coli ribosomes: Evidence for site-specific interaction at U-2504 and G-2502 in domain V of 23S ribosomal RNA (1988) Biochemistry, 27, pp. 3983-3990
Hansen, J.L., Schmeing, T.M., Moore, P.B., Steitz, T.A., Structural insights into peptide bond formation (2002) Proc. Natl. Acad. Sci. USA, 99, pp. 1670-1675
Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Yonath, A., High-resolution structure of the large ribosomal subunit from a mesophilic eubacterium (2001) Cell, 107, pp. 679-688
Hornig, H., Woolley, P., Luhrmann, R., Decoding at the ribosomal A site: Antibiotics, misreading and energy of aminoacyl-tRNA binding (1987) Biochimie, 69, pp. 803-813
Hummel, H., Bock, A., 23S ribosomal RNA mutations in halobacteria conferring resistance to the anti-80S ribosome targeted antibiotic anisomycin (1987) Nucleic Acids Res., 15, pp. 2431-2443
Kim, D.F., Green, R., Base-pairing between 23S rRNA and tRNA in the ribosomal A site (1999) Mol. Cell, 4, pp. 859-864
Kirillov, S., Porse, B.T., Vester, B., Woolley, P., Garrett, R.A., Movement of the 3′-end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics (1997) FEBS Lett., 406, pp. 223-233
Kirillov, S.V., Porse, B.T., Garrett, R.A., Peptidyltransferase antibiotics perturb the relative positioning of the 3′-terminal adenosine of P/P'-site-bound tRNA and 23S rRNA in the ribosome (1999) RNA, 5, pp. 1003-1013
Lazaro, E., Van den Broek, L.A., San Felix, A., Ottenheijm, H.C., Ballesta, J.P., Biochemical and kinetic characteristics of the interaction of the antitumor antibiotic sparsomycin with prokaryotic and eukaryotic ribosomes (1991) Biochemistry, 30, pp. 9642-9648
Lazaro, E., Rodriguez-Fonseca, C., Porse, B., Urena, D., Garrett, R.A., Ballesta, J.P., A sparsomycin-resistant mutant of Halobacterium salinarium lacks a modification at nucleotide U2603 in the peptidyl transferase centre of 23S RNA (1996) J. Mol. Biol., 261, pp. 231-238
Lill, R., Wintermeyer, W., Destabilization of codon-anticodon interaction in the ribosomal exit site (1987) J. Mol. Biol., 196, pp. 137-148
Mankin, A.S., Garrett, R.A., Chloramphenicol resistance mutations in the single 23S rRNA gene of the archaeon H. halobium (1991) J. Bacteriol., 173, pp. 3559-3563
Miskin, R., Zamir, A., Elson, D., The inactivation and reactivation of ribosomal-peptidyltransferase of E. coli (1968) Biochem. Biophys. Res. Commun., 33, pp. 551-557
Moazed, D., Noller, H.F., Intermediate states in the movement of transfer RNA in the ribosome (1989) Nature, 342, pp. 142-148
Monro, R.E., Cerna, J., Marcker, K.A., Ribosome-catalyzed peptidyl transfer: Substrate specificity at the P-site (1968) Proc. Natl. Acad. Sci. USA, 61, pp. 1042-1049
Monro, R.E., Celma, M.L., Vazquez, D., Action of sparsomycin on ribosome-catalysed peptidyl transfer (1969) Nature, 222, pp. 356-358
Nierhaus, K.H., Schulze, H., Cooperman, B.S., Molecular mechanisms of the ribosomal peptidyl transferase center (1980) Biochem. Int., 1, pp. 185-192
Noller, H.F., Hoffarth, V., Zimniak, L., Unusual resistance of peptidyltransferase to protein extraction procedures (1992) Science, 256, pp. 1416-1419
Noller, H.F., Yusupov, M.M., Yusupova, G.Z., Baucom, A., Cate, J.H.D., Translocation of tRNA during protein synthesis (2002) FEBS Lett., 514, pp. 11-16
Odom, O.W., Picking, W.D., Hardesty, B., Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes (1990) Biochemistry, 29, pp. 10734-10744
Ofengand, J., Bakin, A., Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria, and chloroplasts (1997) J. Mol Biol., 266, pp. 246-268
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Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression
Crystal structures of tRNA mimics complexed with the large ribosomal subunit of Deinococcus radiodurans indicate that remote interactions determine the precise orientation of tRNA in the peptidyl-transferase center (PTC). The PTC tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. Sparsomycin binds to A2602 and alters the PTC conformation. H69, the intersubunit-bridge connecting the PTC and decoding site, may also participate in tRNA placement and translocation. A spiral rotation of the 3′ end of the A-site tRNA around a 2-fold axis of symmetry identified within the PTC suggests a unified ribosomal machinery for peptide-bond formation, A-to-P-site translocation, and entrance of nascent proteins into the exit tunnel. Similar 2-fold related regions, detected in all known structures of large ribosomal subunits, indicate the universality of this mechanism.
Crystal structures of tRNA mimics complexed with the large ribosomal subunit of Deinococcus radiodurans indicate that remote interactions determine the precise orientation of tRNA in the peptidyl-transferase center (PTC). The PTC tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. Sparsomycin binds to A2602 and alters the PTC conformation. H69, the intersubunit-bridge connecting the PTC and decoding site, may also participate in tRNA placement and translocation. A spiral rotation of the 3′ end of the A-site tRNA around a 2-fold axis of symmetry identified within the PTC suggests a unified ribosomal machinery for peptide-bond formation, A-to-P-site translocation, and entrance of nascent proteins into the exit tunnel. Similar 2-fold related regions, detected in all known structures of large ribosomal subunits, indicate the universality of this mechanism.
Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression
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Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression
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Martucci NM, Lamberti A, Vitagliano L, Cantiello P, Ruggiero I, Arcari P, Masullo M
* The magic spot ppGpp influences in vitro the molecular and functional properties of the elongation factor 1α from the archaeon Sulfolobus solfataricus (350 views)
Extremophiles (ISSN: 1431-0651, 1433-4909, 1433-4909electronic), 2012 Sep; 16(5): 743-749.
Impact Factor: 2.203
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La Mendola D, Magrì A, Santoro AM, Nicoletti VG, Rizzarelli E
* Copper(II) interaction with peptide fragments of histidine-proline-rich glycoprotein: Speciation, stability and binding details (408 views)
J Chem Res (ISSN: 1873-3344, 0162-0134, 0162-0134print), 2012 Jun; 111: 59-69.
Impact Factor: 3.197
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Improta R, Vitagliano L, Esposito L
* Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures (833 views)
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2011 Sep 16; 6(9): e24533-e24533.
Impact Factor: 4.092
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Merlino A, Russo Krauss I, Castellano I, De Vendittis E, Rossi B, Conte M, Vergara A, Sica F
* Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis (543 views)
J Struct Biol (ISSN: 1047-8477, 1047-8477linking), 2010 Dec; 172(3): 343-352.
Impact Factor: 3.5
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D'Urso L, Grasso G, Messina E, Bongiorno C, Scuderi V, Scalese S, Puglisi O, Spoto G, Compagnini G
* The Role of Linear Carbon Chains in the Aggregation of Copper, Silver, and Gold Nanoparticles (521 views)
J Phys Chem C (ISSN: 1932-7447), 2010 Jan 21; 114(2): 907-915.
Impact Factor: 4.524
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Puglisi A, Rizzarelli E, Vecchio G, Iacovino R, Benedetti E, Pedone C, Saviano M
* Crystal And Molecular Structure Of Beta-Cyclodextrins Functionalized With The Anti-Inflammatory Drug Etodolac (420 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2009 Dec; 91(12): 1227-1235.
Impact Factor: 2.605
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Wekselman I, Davidovich C, Agmon I, Zimmerman E, Rozenberg H, Bashan A, Berisio R, Yonath A
* Ribosome's mode of function: Myths, facts and recent results (395 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2009 Mar; 15(3): 122-130.
Impact Factor: 1.807
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Vaccaro M, Mangiapia G, Accardo A, Tesauro D, Gianolio E, Frielinghaus H, Morelli G, Paduano L
* Polymerized mixed aggregates containing gadolinium complex and CCK8 peptide (429 views)
Colloid Polym Sci (ISSN: 0303-402x), 2008 Dec; 286(14-15): 1643-1652.
Impact Factor: 1.736
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Chambery A, Pisante M, Di Maro A, Di Zazzo E, Ruvo M, Costantini S, Colonna G, Parente A
* Invariant Ser211 is involved in the catalysis of PD-L4, type I RIP from Phytolacca dioica leaves (364 views)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2007 Apr 1; 67(1): 209-218.
Impact Factor: 3.354
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Menchise V, De Simone G, Di Fiore A, Scozzafava A, Supuran CT
* Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of 5-amino-1, 3, 4-thiadiazole-2-sulfonamide and 5-(4-amino-3-chloro-5-fluorophenylsulfonamido)1, 3, 4-thiadiazole-2-sulfon amide to human isoform II (310 views)
Bioorganic & Medicinal Chemistry Letters (ISSN: 0960-894x), 2006 Dec 15; 16(24): 6204-6208.
Impact Factor: 2.538
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Roviello GN, Moccia M, Sapio R, Valente M, Bucci EM, Castiglione M, Pedone C, Perretta G, Benedetti E, Musumeci D
* Synthesis, Characterization And Hybridization Studies Of New Nucleo-Gamma-Peptides Based On Diaminobutyric Acid (493 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2006 Dec; 12(12): 829-835.
Impact Factor: 1.801
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Berisio R, Corti N, Pfister P, Yonath A, Böttger EC
* 23S rRNA 2058A→G alteration mediates ketolide resistance in combination with deletion in L22 (641 views)
Antimicrob Agents Ch (ISSN: 0066-4804, 1098-6596), 2006 Nov; 50(11): 3816-3823.
Impact Factor: 4.153
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Di Fiore A, Pedone C, D'Ambrosio K, Scozzafava A, De Simone G, Supuran CT
* Carbonic anhydrase inhibitors: Valdecoxib binds to a different active site region of the human isoform II as compared to the structurally related cyclooxygenase II 'selective' inhibitor celecoxib (323 views)
Bioorg Med Chem Lett Bioorganic And Medicinal Chemistry Letters (ISSN: 0960-894x), 2006 Jan 15; 16(2): 437-442.
Impact Factor: 2.538
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Berisio R, Granata V, Vitagliano L, Zagari A
* Imino acids and collagen triple helix stability: Characterization of collagen-like polypeptides containing Hyp-Hyp-Gly sequence repeats (438 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2004 Sep 22; 126(37): 11402-11403.
Impact Factor: 6.903
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Agmon I, Amit M, Auerbach T, Bashan A, Baram D, Bartels H, Berisio R, Greenberg I, Harms J, Hansen HAS, Kessler M, Pyetan E, Schluenzen F, Sittner A, Yonath A, Zarivach R
* Ribosomal crystallography: A flexible nucleotide anchoring tRNA translocation, facilitates peptide-bond formation, chirality discrimination and antibiotics synergism (312 views)
Febs Lett (ISSN: 0014-5793, 0014-5793print, 1873-3468electronic), 2004 Jun 1; 567(1): 20-26.
Impact Factor: 3.843
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Improta R, Barone V
* Interplay of electronic, environmental, and vibrational effects in determining the hyperfine coupling constants of organic free radicals (298 views)
Chem Rev (ISSN: 0009-2665), 2004 Mar; 104(3): 1231-1253.
Impact Factor: 20.233
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Rossi F, Zanotti G, Saviano M, Iacovino R, Palladino P, Saviano G, Amodeo P, Tancredi T, Laccetti P, Corbier C, Benedetti E
* New antitumour cyclic astin analogues: Synthesis, conformation and bioactivity (454 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2004 Feb; 10(2): 92-102.
Impact Factor: 1.652
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Improta R, Santoro F, Dietl C, Papastathopoulos E, Gerber G
* Time dependent DFT investigation on the two lowest 1B u states of the trans isomer of stilbene and stiff-stilbenes (349 views)
Chem Phys Lett (ISSN: 0009-2614), 2004; 387(4-6): 509-516.
Impact Factor: 2.438
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Bashan A, Zarivach R, Schluenzen F, Agmon I, Harms J, Auerbach T, Baram D, Berisio R, Bartels H, Hansen HAS, Fucini P, Wilson D, Peretz M, Kessler M, Yonath A
* Ribosomal crystallography: Peptide bond formation and its inhibition (588 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2003 Sep; 70(1): 19-41.
Impact Factor: 2.733
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Berisio R, Schluenzen F, Harms J, Bashan A, Auerbach T, Baram D, Yonath A
* Structural insight into the role of the ribosomal tunnel in cellular regulation (378 views)
Nat Struct Biol (ISSN: 1072-8368), 2003 May; 10(5): 366-370.
Impact Factor: 11.579
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Bonomo RP, Bruno V, Conte E, De Guidi G, La Mendola D, Maccarrone G, Nicoletti F, Rizzarelli E, Sortino S, Vecchio G
* Potentiometric, spectroscopic and antioxidant activity studies of SOD mimics containing carnosine (385 views)
Dalton T (ISSN: 1477-9226, 1477-9234, 1477-9234electronic), 2003; (23): 4406-4415.
Impact Factor: 2.908
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Menziani MC, De Benedetti PG, Langella E, Barone V
* Seeking for binding determinants of the prion protein to human plasminogen (407 views)
Mol Phys (ISSN: 0026-8976), 2003; 101(17): 2763-2773.
Impact Factor: 1.591
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Masullo M, Cantiello P, Paola B, Fiengo A, Vitagliano L, Zagari A, Arcari P
* Valine114 Replacements In The Archaeal Elongation Factor 1a Enhanced Its Ability To Interact With Aminoacyl-Trna And Kirromycin (353 views)
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2002; 41(49): 14482-14488.
Impact Factor: 4.064
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Esposito L, Vitagliano L, Zagari A, Mazzarella L
Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures (301 views)
Protein Eng (ISSN: 0269-2139, 0269-2139print, 0269-2139linking), 2000 Dec; 13(12): 825-828.
Impact Factor: 2.442
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D'Andrea LD, Mazzeo M, Isernia C, Rossi F, Saviano M, Gallo P, Paolillo L, Pedone C
Solution conformational preferences of a peptidic analogue of a natural macrolide (382 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 1997; 42(3): 349-361.
Impact Factor: 2.425
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Pavone V, Lombardi A, Saviano M, Nastri F, Fattorusso R, Maglio O, Isernia C, Paolillo L, Pedone C
β-alanine containing cyclic peptides with turned structure: The 'pseudo type II β-turn. ' VI (463 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 1994 Nov; 34(11): 1517-1526.
Impact Factor: 2.425
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Bustamante C, Gurrieri S, Pasternack RF, Purrello R, Rizzarelli E
Interaction of water-soluble porphyrins with single- and double-stranded polyribonucleotides (396 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 1994 Sep; 34(8): 1099-1104.
Impact Factor: 2.425
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Romano M, Cerra M, Salvatore M, Onorati A
Effects of ionizing radiations on the activity of valyl tRNA synthetase isolated from rat liver and from Morris hepatoma 7777 (834 views)
Tumori (ISSN: 0300-8916, 0300-8916print, 0300-8916linking), 1974 Jul; 60(4): 301-306.
Impact Factor: 0.408
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33 Records (32 excluding Abstracts).
Total impact factor: 122.041 (117.949 excluding Abstracts).
Total 5 year impact factor: 162.846 (158.309 excluding Abstracts).
Total impact factor: 122.041 (117.949 excluding Abstracts).
Total 5 year impact factor: 162.846 (158.309 excluding Abstracts).
465 views. Last view on Saturday 06 May 2023, 8:38:26
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