Peptidyl Transferase Center

Aminohexose Nucleosides. The 4-aminohexose nucleosides (128—140) are Hsted in Table 7 (1—4,240—242). A biosynthetic relationship between the 4-aminohexose peptidyl nucleoside antibiotics and the pentopyranines has been proposed (1). The 4-aminohexose pyrimidine nucleoside antibiotics block peptidyl transferase activity and inhibit transfer of amino acids from aminoacyl-tRNA to polypeptides. Hikizimycin, gougerotin, amicetin, and blasticidin S bind to the peptidyl transferase center at overlapping sites (243). 

Macrolides are a group of antibiotics, produced in nature by many actinomycetes strains, that are composed of a 12- to 16-membered lactone ring, to which one or more sugar substituents is attached. They target the peptidyl transferase center on the 50S ribosomal subunit and function primarily by interfering with movement of the nascent peptide away from the active site and into the exit tunnel. 

Ribosomal Protein Synthesis Inhibitors. Figure 5 Nucleotides at the binding sites of chloramphenicol, erythromycin and clindamycin at the peptidyl transferase center. The nucleotides that are within 4.4 A of the antibiotics chloramphenicol, erythromycin and clindamycin in 50S-antibiotic complexes are indicated with the letters C, E, and L, respectively, on the secondary structure of the peptidyl transferase loop region of 23S rRNA (the sequence shown is that of E. coll). The sites of drug resistance in one or more peptidyl transferase antibiotics due to base changes (solid circles) and lack of modification (solid square) are indicated. Nucleotides that display altered chemical reactivity in the presence of one or more peptidyl transferase antibiotics are boxed. 

Penicillin Binding Protein Pentasaccharide Peptide Mass Fingerprint Peptide YY Peptidoglycans Peptidyl Transferase Center Peptidyl-Dipeptidase PERI... 

During the normal process of termination of translation, stop codons are recognized by protein release factors (RF). Although the details of the process are not fully understood, it is believed that when a termination codon reaches the ribosomal A-site, the RF associates with the ribosomal-mRNA complex, inducing the peptidyl-transferase center to hydrolyze the ester bond of the pepti-... 

Long KS, Hansen LH, Jakobsen L, Vester B. (2006) Interaction of pleuro-mutilin derivatives with the ribosomal peptidyl transferase center. Antimicrob Agents Chemother 50 1458-1462. 

Abbreviations aa-tRNA Amino-acyl tRNA eLF Eukaryotic translation initiation factor IF Prokaryotic translation initiation factor eEF Eukaryotic translation elongation factor EF Prokaryotic translation elongation factor eRF Eukaryotic translation termination factor (release factor) RF Prokaryotic translation release factor RRF Ribosome recycling factor Rps Protein of the prokaryotic small ribosomal subunit Rpl Protein of the eukaryotic large ribosomal subunit S Protein of the prokaryotic small ribosomal subunit L Protein of the prokaryotic large ribosomal subunit PTC Peptidyl transferase center RNC Ribosome-nascent chain-mRNA complex ram Ribosomal ambiguity mutation RAC Ribosome-associated complex NMD Nonsense-mediated mRNA decay... 

The consequence of release factor recognition of a termination codon in the A site is to alter the peptidyl transferase center on the large ribosomal subunit so that it can accept water as the attacking nucleophile rather than requiring the normal substrate, aminoacyl-tRNA (fig. 29.20). In other... 

Narciclasine (215) is an antitumor agent which exerts an antimitotic effect during metaphase by immediately terminating protein synthesis in eukaryotic cells at the step of peptide bond formation (97,101,141,142), apparently by interaction with the ansiomycin area of the ribosomal peptidyl transferase center (142). The alkaloid has also been found to inhibit HeLa cell growth and to stabilize HeLa cell polysomes in vivo (97). Although DNA synthesis was retarded by narciclasine, RNA synthesis was practically unaffected (97,142). Sev-... 

Muth, G.W., Ortoleva-Donnelly, L. and Strobel, S.A. (2000) A single adenosine with a neutral pFCa in the ribosomal peptidyl transferase center. Science, 289, 947. 

To stop the translation reaction and further stabilize the ribosomal complexes, cycloheximide can be added in the eukaryotic system (Gersuk et al., 1997). For the same purpose chloramphenicol, an antibiotic that inhibits bacterial protein synthesis by binding to the 23S ribosomal RNA in the peptidyl transferase center, can be used in the E. coli system (Mattheakis et al., 1994). However, chloramphenicol was found to have no influence on the efficiency of E. coli ribosome display (Hanes and Pluckthun, 1997). 

Fig. 4.1 Overview of ribosome. Center These space filled representations are based on docking of the large ribosomal subunit [1] (grey RNA and blue protein) onto the small subunit [2] (yellow RNA and green protein) based on a protein alpha carbon and rRNA phosphate backbone trace of the 70S ribosome bound with tRNA [53]. Functional sites are circled and labeled according to the corresponding bound tRNA molecules A-site (red), P-site (orange), E-site (purple) and factor binding site (FBS). Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) that is located on the large subunit between the A-site and P-site. Left The...

Most antibiotics that inhibit the function of the SOS subunit bind near its peptidyl transferase center (Fig. 4.4) and block peptide bond formation. Crystal structures are available for several such antibiotics bound to the ribosome (Fig. 4.5). They appear to inhibit the peptidyl transferase reaction either by competing directly with its substrates for binding, or indirectly by blocking the exit tunnel. 

Two hydrophobic crevices near the peptidyl transferase center appear to be particularly important for antibiotic binding (Figs. 4.4 and 4.5). The first hydrophobic crevice, which is at the peptidyl transferase center, normally functions as the binding site for amino acid side chains of A-site substrates [11, 16], Antibiotics that bind to this site will block the binding with A-site substrates and thereby directly... 

Fig. 4.5 Overview of antibiotics bound at the peptidyl transferase center. A surface representation of the large subunit of H. marismortui includes the P-site, A-site and entrance to the peptide exit tunnel. Most of these antibiotics contact either the active site hydro-phobic crevice (green surface, upper center) or the hydrophobic crevice at the entrance to the exit tunnel (green surface, lower right). In addition, many of these antibiotics occupy an elongated pocket (dark surface, center) in the wall of the exit tunnel between these two crevices. The antibiotics shown are all from complexes with H. marismortui ribosomes and overlap the binding site of A-site substrates (red sticks) or of a P-site substrates (orange sticks). Fig. modified from...

Fig. 4.7 Superposition of macrolides. A cutaway view of a space-filled representation of rRNA (gray) and protein (light blue) show the peptide exit tunnel (left) and the peptidyl transferase center (upper right) of H. maris-mortui. The lactone rings of tylosin (orange sticks), carbomycin A (red sticks), spiramycin (yellow sticks) and azithromycin (light blue sticks) become superimposed when rRNA is superimposed among these structures. The lactone rings bind to the hydrophobic crevice...

In the crystal structure, blasticidin S binds to two sites on the ribosome (Fig. 4.13) and forms base-pairs with Hm G2284 and G2285 Ec 2251 and 2252). These two guanines are almost totally conserved residues of the P-loop, and are known to base pair with the CCA end of tRNA in order to position the P-site substrate in the peptidyl transferase center [47]. 

Hansen, J. L, Moore, P., Steitz, X, Cocrystal stmctures of five antibiotics botmd at the peptidyl transferase center of the 50S ribosomal subunit. J. Mol. 

Tan, G.T., DeBlasio, A., Mankin, A.S., Mutations in the peptidyl transferase center of 23 S rRNA reveal the site of action of sparsomydn, a universal inhibitor of translation./. Mol. Biol. 1996, 263, 222-230. 

A tunneTYpore starting at the peptidyl transferase center on the ribosome and ending on the solvent side on the large ribosomal subunit. See Gabashvili,... 

Cruz-Vera LR, Gong M, Yanofsky C. Changes produced by bound tryptophan in the ribosome peptidyl transferase center in response to TnaC, a nascent leader peptide. Proc. Natl. Acad. Sci. U.S.A. 2006 103 3598-3603. 

Cruz-Vera LR, New A, Squires C, Yanofsky C. Ribosomal features essential for tna operon induction tryptophan binding at the peptidyl transferase center. J Bacteriol. 2007 189 3140-3146. 

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