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2'(3')-O-(N-formylmethionyl)-adenosine-5'-phosphate + CACCA-Phe
?
-
-
-
-
?
acetylphenylalanyl-tRNA + puromycin
acetylphenylalanyl-puromycin + tRNA
-
-
-
-
?
AcPhe-tRNA + pCpCp-puromycin
tRNA + AcPhe-pCpCp-puromycin
-
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
cytidylyl-(3',5'-phosphoryl)-3'-amino-3'-deoxy-3'-L-beta,beta-difluorophenylalanyl-N6,N6-dimethyladenosine + ?
?
-
-
-
-
?
cytidylyl-(3',5'-phosphoryl)-3'-amino-3'-deoxy-3'-L-phenylalanyl-N6,N6-dimethyladenosine + ?
?
-
-
-
-
?
fMet-Phe-tRNAPhe + puromycin
tRNAPhe + fMet-Phe-puromycin
fMet-tRNAfMet + Phe-tRNAPhe
tRNAfMet + fMet(Phe-tRNA2)
fMet-Val-tRNAVal + Phe-tRNAPhe
tRNAVal + fMet-Val(Phe-tRNA2)
formyl-Met-tRNA + puromycin
tRNA + formyl-Met-puromycin
-
-
-
-
ir
formylmethionyl-tRNA + alpha-hydroxy-puromycin
tRNA + formylmethionyl-alpha-hydroxy-puromycin
-
ester linkage
-
?
formylmethionyl-tRNA + puromycin
tRNA + formylmethionyl-puromycin
GlcNAc-MurNGlyc-L-Ala1-D-iGln2-meso-DapNH23-D-Ala4 + D-methionine
GlcNAc-MurNGlyc-L-Ala1-D-iGln2-meso-DapNH23-D-Met4 + D-alanine
-
-
-
-
?
L-Phe-tRNA + puromycin
tRNA + L-Phe-puromycin
-
-
-
-
?
Lys-tRNALys + Phe-tRNAPhe
tRNALys + Lys(Phe-tRNA2)
-
-
-
-
?
Lys-tRNALys + puromycin
tRNALys + Lys-puromycin
-
-
-
-
?
Met-Phe-tRNAPhe + Phe-tRNAPhe
tRNAPhe + Met-Phe(Phe-tRNA2)
-
-
-
-
?
Met-tRNA + cytidine-cytidine-hydroxypuromycin
tRNA + Met-cytidine-cytidine-hydroxypuromycin
-
-
-
-
?
Met-tRNA + cytidine-cytidineadenosine-phenylalanine-caproic acid
?
-
-
-
-
?
Met-tRNA + cytidine-hydroxypuromycin
tRNA + Met-cytidine-hydroxypuromycin
-
-
-
-
?
Met-tRNA + cytidine-puromycin
tRNA + Met-cytidine-puromycin
-
-
-
-
?
Met-tRNA + puromycin
tRNA + Met-puromycin
-
-
-
-
?
N-AcMet-tRNA + puromycin
tRNA + N-AcMet-puromycin
-
-
-
?
N-AcPhe-tRNA + puromycin
tRNA + N-AcPhe-puromycin
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl-aminoacyl-tRNA2
phenylalanyl-tRNA + puromycin
tRNA + phenylalanyl-puromycin
polylysyl-tRNA + puromycin
tRNA + polylysyl-puromycin
polyphenylalanyl-tRNA + puromycin
tRNA + polyphenylalanyl-puromycin
-
-
-
?
additional information
?
-
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
reaction only in the presence of 70S ribosomes and the appropriate mRNA
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-70S ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-70S ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-70S ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-70S ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-80S ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-80S ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
AcPhe-tRNA-polyU-80S ribosome complex
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
-
-
-
-
?
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
-
-
-
?
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
-
fragment reaction
-
?
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
-
fragment reaction
-
?
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
-
fragment reaction
-
?
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
-
-
-
?
fMet-Phe-tRNAPhe + puromycin
tRNAPhe + fMet-Phe-puromycin
-
-
-
-
?
fMet-Phe-tRNAPhe + puromycin
tRNAPhe + fMet-Phe-puromycin
-
-
-
-
?
fMet-tRNAfMet + Phe-tRNAPhe
tRNAfMet + fMet(Phe-tRNA2)
-
-
-
-
?
fMet-tRNAfMet + Phe-tRNAPhe
tRNAfMet + fMet(Phe-tRNA2)
-
-
-
-
?
fMet-Val-tRNAVal + Phe-tRNAPhe
tRNAVal + fMet-Val(Phe-tRNA2)
-
-
-
-
?
fMet-Val-tRNAVal + Phe-tRNAPhe
tRNAVal + fMet-Val(Phe-tRNA2)
-
-
-
-
?
formylmethionyl-tRNA + puromycin
tRNA + formylmethionyl-puromycin
-
-
-
?
formylmethionyl-tRNA + puromycin
tRNA + formylmethionyl-puromycin
-
formylmethionyl-tRNA-AUG-70S ribosome complex
-
?
N-AcPhe-tRNA + puromycin
tRNA + N-AcPhe-puromycin
-
-
-
?
N-AcPhe-tRNA + puromycin
tRNA + N-AcPhe-puromycin
-
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
-
?
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
the enzyme forms L-Lys3->D-iAsn-L-Lys3 cross-links following cleavage of the L-Lys3-D-Ala4 peptide bond of the donor stem tetrapeptide
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
the enzyme is highly specific for acyl donors containing a stem tetrapeptide ending in L-Lys3-D-Ala4 and for acyl acceptors containing a D-iAsn substituted L-Lys3 at the third position of the stem peptide
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
the enzyme synthesizes diaminopimelic acid (DAP)-DAP cross-links by the removal of the fourth D-alanine residue of an acyl donor tetrapeptide stem and the attachment of the remaining meso-DAP residue to the meso-DAP residue of a second acyl acceptor peptide
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl-aminoacyl-tRNA2
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl-aminoacyl-tRNA2
-
-
-
-
?
phenylalanyl-tRNA + puromycin
tRNA + phenylalanyl-puromycin
-
poly-U-directed translation system
-
?
phenylalanyl-tRNA + puromycin
tRNA + phenylalanyl-puromycin
-
poly-U-directed translation system
-
?
polylysyl-tRNA + puromycin
tRNA + polylysyl-puromycin
-
-
-
?
polylysyl-tRNA + puromycin
tRNA + polylysyl-puromycin
-
reaction only in the presence of 70S ribosomes and the appropriate mRNA
-
?
additional information
?
-
-
in the presence of elongation factor EF-G with GTP the poly-U-directed translation is much more resistant to inhibitors of the peptidyl-transferase
-
-
?
additional information
?
-
-
the nature of the side-chain of A-aa acceptor substrates strongly affects the acceptor activity in the peptidyl transfer reaction on the ribosome. This activity is furthermore affected by the nature of the P-site donor. The most efficient (A-Phe) and the least active (A-Gly, A-DPhe) acceptors are, the same in all three donor configurations so far systematically tested. With Lys(n)-tRNA on the P-site, A-Phe has a catalytic rate constant (kcat) about 50-100fold higher than A-Gly. A-Phe has approximately the same acceptor activity as Pm, for which kcat has independently been established to about 5/sec with Met-Phe-tRNAPhe as the donor substrate, under standard conditions. The D-enantiomers of amino acids with only one carbon atom in the side-chain (Ala, Ser, and Cys) are all incorporated almost as efficiently as their L-enantiomer counterparts. With alanyl-tRNA as the A-site substrate, the Calpha pinching mechanism can orient both L- and D-enantiomers for nucleophilic attack. Substrate specificity, detailed overview. Puromycin (Pm) and analogues still react in the uninduced state plausibly because ribosome residue U2585 forms a hydrogen bond with Pm(2'-OH), thus opening the gate for nucleophilic attack without full induction
-
-
-
additional information
?
-
-
the peptidyl transferase reaction is monitored by fMet-Phe dipeptide, fMet-Phe-puromycin, and fMet-Val-Phe tripeptide formation assays
-
-
-
additional information
?
-
-
in the presence of elongation factor EF-G with GTP the poly-U-directed translation is much more resistant to inhibitors of the peptidyl-transferase
-
-
?
additional information
?
-
-
no activity with GlcNAc-MurNGlyc-L-Ala1-DiGln2-meso-DapNH23-D-Ala4-D-Ala5
-
-
?
additional information
?
-
the enzyme shows hydrolytic activity with nitrocefin (Km of 0.097 mM, kcat of 0.013 s-1, and kcat/Km of 145 1/sec*mM, at pH 10.0)
-
-
?
additional information
?
-
-
the enzyme shows hydrolytic activity with nitrocefin (Km of 0.097 mM, kcat of 0.013 s-1, and kcat/Km of 145 1/sec*mM, at pH 10.0)
-
-
?
additional information
?
-
-
the five isoforms are active in assays of peptidoglycan cross-linking (Mt5), beta-lactam acylation (Mt3), or both (Mt1, Mt2, and Mt4). Mt3 is the only isoform that is inactive in the crosslinking assay
-
-
?
additional information
?
-
the enzyme shows hydrolytic activity with nitrocefin (Km of 0.097 mM, kcat of 0.013 s-1, and kcat/Km of 145 1/sec*mM, at pH 10.0)
-
-
?
additional information
?
-
-
the peptidyltransferase center is the catalytic heart of the ribosome and its inner core is composed of five universally conserved 23S rRNA residues
-
-
?
additional information
?
-
-
deletion of ribosomal protein L27 is predicted to give only a minor reaction rate reduction. The N-terminus of L27 interacts with the A76 phosphate group of the A-site tRNA, explaining the observed impairment of A-site substrate binding for ribosomes lacking L27. The calculated energetics show that substrate puromycin can cause a downward pKa shift of L27 and that the reaction proceeds faster with the L27 N-terminus deprotonated, in contrast to the situation with aminoacyl-tRNA substrates. These results could explain the observed differences in pH dependence between the puromycin and C-puromycin reactions, where the former reaction has been seen to depend on an additional ionizing group besides the attacking amine, and this ionizing group is predicted to be the N-terminal amine of L27
-
-
?
additional information
?
-
-
the peptidyl transferase reaction is monitored by fMet-Phe dipeptide, fMet-Phe-puromycin, and fMet-Val-Phe tripeptide formation assays
-
-
-
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1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine
1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine
40S subunits of ribosomes
-
inhibition proportional to the 40S-subunit-concentration
-
ampicillin
-
strain 18sH Con-, 60 microg/ml, 50 percent inhibition; strain 18s SAI-, 3 microg/ml, 50 percent inhibition
arginine attenuator peptide
-
the wild type arginine attenuator peptide (AAP) inhibits peptidyl transferase center (PTC) function. AAP containing the D12N mutation, which eliminates Arg-induced ribosome stalling, also eliminates Arg's effect on PTC function
-
Bamicetin
-
complete inhibition with AcPhe-tRNA as donor, with polylysyl-tRNA as donor less active
benzyl penicillin
-
strain 18sH Con-, 450 microg/ml, 50 percent inhibition; strain 18s SAI-, 0.3 microg/ml, 50 percent inhibition
carbenicillin
-
strain 18sH Con-, 50 microg/ml, 50 percent inhibition; strain 18s SAI-, 0.2 microg/ml, 50 percent inhibition
cephaloridine
-
strain 18sH Con-, 200 microg/ml, 50 percent inhibition; strain 18s SAI-, 0.1 microg/ml, 50 percent inhibition
chlortetracycline
-
59% inhibition
cytidylyl(3'-5')2'(3')-O-(alpha-aminoisobutyryl)adenosine
-
-
cytidylyl(3'-5')2'(3')-O-cycloleucyladenosine
-
-
cytidylyl-3'-5'-/2'(3')-O-L-phenylalanyl/L-adenosine
-
50% inhibition of peptidyltransferase, inhibition can be reversed by increasing concentration of puromycin
Gly-chloramphenicol
-
competitive inhibition with acetylphenylalanyl-tRNA-polyU-ribosome complex, newly formed complex is inactive towards puromycin
Gly-Phe-chloramphenicol
-
competitive inhibition with acetylphenylalanyl-tRNA-polyU-ribosome complex, newly formed complex is inactive towards puromycin
L-Phe-chloramphenicol
-
competitive inhibition with acetylphenylalanyl-tRNA-polyU-ribosome complex, newly formed complex is inactive towards puromycin
L-Phe-Gly-chloramphenicol
-
competitive inhibition with acetylphenylalanyl-tRNA-polyU-ribosome complex, newly formed complex is inactive towards puromycin
m-nitrophenylboric acid
-
more potent inhibitor than phenylboric acid
N1,N12-Diacetylspermine
-
both stimulatory and inhibitory effects at the kinetic phase in the presence of the factors washable from ribosomes, depending on ligand concentration
N1,N12-dipivaloylspermine
-
both stimulatory and inhibitory effects at the kinetic phase in the presence of the factors washable from ribosomes, depending on ligand concentration
N1-acetylspermine
-
both stimulatory and inhibitory effects at the kinetic phase in the presence of the factors washable from ribosomes, depending on ligand concentration
Oxamicetin
-
more potent than amicetin
1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine
-
i.e. ZINC19595411
1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine
-
i.e. ZINC19595411
1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine
-
i.e. ZINC19595411
1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine
-
i.e. ZINC22812775
1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine
-
i.e. ZINC22812775
1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine
-
i.e. ZINC22812775
Amicetin
-
complete inhibition with AcPhe-tRNA as donor, with polylysyl-tRNA as donor less active
Amicetin
-
less potent than oxamicetin
anisomycin
-
inhibition of formation of AcPhe-puromycin catalyzed by rabbit reticulocyte ribosomes
blasticidin S
-
-
blasticidin S
-
inhibition of formation of Ac-Phe-puromycin catalyzed by rabbit reticulocyte ribosomes
carbomycin
-
-
chloramphenicol
-
-
chloramphenicol
-
50% inhibition
chloramphenicol
-
competitive inhibition with acetylphenylalanyl-tRNA-polyU-ribosome complex, newly formed complex is inactive towards puromycin
chloramphenicol
-
CHL, inhibits protein synthesis by targeting the peptidyl transferase center of the bacterial ribosome. Analysis of the binding site of CHL in the peptidyl transferase center of the 50S ribosomal subunit, overview. The identity of the penultimate residue of the nascent peptide is critical for the inhibitory activity, specificity and mechanism
chloramphenicol
-
weak peptide bond formation inhibition only by ribosomes with A2451C, A2451U or A2451G, peptide bond formation inhibition by ribosomes with G2447A is essentially unimpaired
clindamycin
-
-
doripenem
-
-
eperezolid
-
ZINC03813328
eperezolid
-
ZINC03813328
eperezolid
-
ZINC03813328
ertapenem
-
-
Imipenem
-
-
linezolid
-
binds in the A site pocket at the peptidyltransferase center of the ribosome overlapping the aminoacyl moiety of an A-site bound tRNA as well as many clinically important antibiotics. Binding of linezolid stabilizes a distinct conformation of the universally conserved 23S rRNA nucleotide U2585 that would be nonproductive for peptide bond formation. In a model oxazolidinones impart their inhibitory effect by perturbing the correct positioning of tRNAs on the ribosome
linezolid
-
LZD, inhibits protein synthesis by targeting the peptidyl transferase center of the bacterial ribosome. Analysis of the binding site of LZD in the peptidyl transferase center of the 50S ribosomal subunit, overview. The identity of the penultimate residue of the nascent peptide is critical for the inhibitory activity, specificity and mechanism
madumycin II
-
i.e. MADU, an alanine-containing streptogramin A antibiotic, inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. It allows binding of the tRNAs to the ribosomal A and P sites, but prevents correct positioning of their CCA-ends into the PTC thus making peptide bond formation impossible. Drug-induced rearrangement of nucleotides U2506 and U2585 of the 23S rRNA resulting in the formation of the U2506-G2583 wobble pair that is attributed to a catalytically inactive state of the PTC. At 0.005 mM concentration, MADU reduces the efficiency of protein synthesis by over 100fold
madumycin II
-
i.e. MADU, an alanine-containing streptogramin A antibiotic, inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. It allows binding of the tRNAs to the ribosomal A and P sites, but prevents correct positioning of their CCA-ends into the PTC thus making peptide bond formation impossible. Drug-induced rearrangement of nucleotides U2506 and U2585 of the 23S rRNA resulting in the formation of the U2506-G2583 wobble pair that is attributed to a catalytically inactive state of the PTC. Structures of inhibitor madumycin II in complex with the 70S ribosome and A- and P-tRNAs, overview
meropenem
-
-
posizolid
-
ZINC03982517
radezolid
-
-
sparsomycin
-
-
sparsomycin
-
binds to 50S bacterial ribosomal subunit. Calculated binding free energy is about -6 kcal/mol. In the simulation protocol, restraining potentials are activated for the orientational and translational movements of the ligand relative to the binding site when it is decoupled from the binding pocket, and then released once the ligand fully interacts with the rest of the system. The number of water molecules in the binding pocket is allowed to fluctuate dynamically in response to the ligand during the calculations
sparsomycin
-
inhibition of formation of AcPhe-puromycin catalyzed by rabbit reticulocyte ribosomes
spermine
-
competitive inhibitor of peptide bond formation at the kinetic phase of the puromycin reaction
spermine
-
in the absence of factors washable from ribosomes
streptogramin A
-
-
sutezolid
-
ZINC03810825
tedizolid
-
ZINC43100953
tiamulin
-
-
valnemulin
-
single mutations at positions 2055, 2447, 2504 and 2572, Escherichia coli numbering, of 23S rRNA each confer a significant and similar degree of valnemulin resistance
ZINC19944344
-
-
ZINC19944344
-
low inhibition
ZINC35154793
-
-
ZINC37712815
-
-
ZINC37712815
-
low inhibition
ZINC37713642
-
-
ZINC37715345
-
-
ZINC54418966
-
-
ZINC71794395
-
-
ZINC90290472
-
-
ZINC90290472
-
low inhibition
additional information
-
streptogramins A is a class of protein synthesis inhibitors that target the peptidyl transferase center (PTC) on the large subunit of the ribosome
-
additional information
-
reevaluation of the mechanism of inducible CHL resistance. CHL and LZD poorly inhibit peptide bond formation when glycine residues are involved. Induction of CHL resistance genes relies on the stimulatory effect of the penultimate residue of the nascent chain on drug action
-
additional information
-
improved small molecule inhibitors of the Mtb ribosomal PTC are obtained using a combination of NMR transverse relaxation times (T2) and computational chemistry approaches, inhibitor design from scaffolds, docking study, overview. Two phenylthiazole derivatives with low IC50 values are predicted by machine learning models as effective inhibitors. Screening of the ZINC database. Predicted binding of oxazolidinone antibiotics that target the ribosomal PTC
-
additional information
-
improved small molecule inhibitors of the Mtb ribosomal PTC are obtained using a combination of NMR transverse relaxation times (T2) and computational chemistry approaches, inhibitor design from scaffolds, overview. Two phenylthiazole derivatives with low IC50 values are predicted by machine learning models as effective inhibitors. Screening of the ZINC database. Predicted binding of oxazolidinone antibiotics that target the ribosomal PTC
-
additional information
-
the peptidyl transferase center is not inhibited by D-arginine
-
additional information
-
improved small molecule inhibitors of the Mtb ribosomal PTC are obtained using a combination of NMR transverse relaxation times (T2) and computational chemistry approaches, inhibitor design from scaffolds, docking study, overview. Two phenylthiazole derivatives with low IC50 values are predicted by machine learning models as effective inhibitors. Screening of the ZINC database. Molecular docking of Mycobacterium tuberculosis-homologous Staphylococcus aureus peptidyl transferase center (PTC). Predicted binding of oxazolidinone antibiotics that target the ribosomal PTC
-
additional information
-
streptogramins A is a class of protein synthesis inhibitors that target the peptidyl transferase center (PTC) on the large subunit of the ribosome. In ribosome complex with mRNA and tRNAs, the binding site of madumycin II is very similar to the binding sites of virginiamycin M, dalfopristin, or flopristin (all proline-containing type A streptogramin antibiotics)
-
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evolution
-
for the ribosomal PTC used (U2673-C2836), there is 100% identity between Mycobacterium tuberculosis and Mycobacterium smegmatis. The Staphylococcus aureus peptidyl transferase center (PTC) is homologous to Mycobacterium tuberculosis PTC
evolution
-
reconstruction of the three-dimensional structure of the ancestral peptidyl transferase center (PTC) built by concatamers of ancestral sequences of tRNAs, analysis of its possible interactions with tRNAs molecules, three-dimensional modeling, overview. Docking experiments between the ancestral PTC and tRNAs suggest that in the origin of the translation system, the PTC functioned as an adhesion center for tRNA molecules. Structure PDB ID4V8X is used as a template. The origin of the translation system is a major evolutionary transition because it enabled the establishment of the ribonucleoprotein world. The transfer RNA (tRNA) molecule played a central role during the origin of translation, bridging RNA and (RNA + proteins) worlds. These tRNAs may offer clues towards the elucidation of the origin of the genetic code. The ribosome is also at the core of this process: more specifically, the PTC responsible for peptide bond formation. The PTC is perhaps the oldest ribozyme due to its essential function of protein synthesis and because it is highly conserved in all cellular organisms. Since natural selection works without anticipation, the early PTC could have acted as a ribozyme that randomly produced peptide chains
evolution
-
the Staphylococcus aureus peptidyl transferase center (PTC) is homologous to Mycobacterium tuberculosis PTC
evolution
-
for the ribosomal PTC used (U2673-C2836), there is 100% identity between Mycobacterium tuberculosis and Mycobacterium smegmatis. The Staphylococcus aureus peptidyl transferase center (PTC) is homologous to Mycobacterium tuberculosis PTC
-
evolution
-
for the ribosomal PTC used (U2673-C2836), there is 100% identity between Mycobacterium tuberculosis and Mycobacterium smegmatis. The Staphylococcus aureus peptidyl transferase center (PTC) is homologous to Mycobacterium tuberculosis PTC
-
malfunction
-
bypass of classical penicillin-binding proteins by the L,D-transpeptidase leads to high-level ampicillin resistance in Enterococcus faecium mutants
malfunction
-
loss of L,D-transpeptidase gene MT2594 does not alter susceptibility to isoniazid and D-cycloserine, but is associated with increased susceptibility to amoxicillin in the presence of clavulanic acid
malfunction
Mycobacterium tuberculosis lacking a functional copy of LdtMt5 displays aberrant growth and is more susceptible to killing by crystal violet, osmotic shock, and select carbapenem antibiotics
malfunction
-
loss of L,D-transpeptidase gene MT2594 does not alter susceptibility to isoniazid and D-cycloserine, but is associated with increased susceptibility to amoxicillin in the presence of clavulanic acid
-
malfunction
-
Mycobacterium tuberculosis lacking a functional copy of LdtMt5 displays aberrant growth and is more susceptible to killing by crystal violet, osmotic shock, and select carbapenem antibiotics
-
malfunction
-
bypass of classical penicillin-binding proteins by the L,D-transpeptidase leads to high-level ampicillin resistance in Enterococcus faecium mutants
-
metabolism
-
the peptidoglycans of the rough and smooth morphotypes contain predominantly 3->3 cross-links generated by L,D-transpeptidases
metabolism
-
mechanism of peptidyltransferase centre (PTC) completion, overview. Requirement of the universally conserved Gly-Gly-Gln (GGQ) tripeptide in the highly conserved peptidyl transferase center suggesting that the reported conformation is likely shared during termination of protein synthesis in all domains of life
metabolism
mechanism of peptidyltransferase centre (PTC) completion, overview. Requirement of the universally conserved Gly-Gly-Gln (GGQ) tripeptide in the highly conserved peptidyl transferase center suggesting that the reported conformation is likely shared during termination of protein synthesis in all domains of life
metabolism
-
the peptidoglycans of the rough and smooth morphotypes contain predominantly 3->3 cross-links generated by L,D-transpeptidases
-
physiological function
-
changes of 23S rRNA nucleotides in the 2585 region of the peptidyl transferase center, G2583A and U2584C, reduce maximum induction of tna operon expression by tryptophan in vivo without affecting the concentration of tryptophan necessary to obtain 50% induction. The growth rate of strains with ribosomes with either of these changes is not altered appreciably. In vitro analyses show that tryptophan is not as efficient in protecting TnaC-tRNAPro from puromycin action as wild-type ribosomes. However, added tryptophan does prevent sparsomycin action as it normally does with wild-type ribosomes. These two mutational changes act by reducing the ability of ribosome-bound tryptophan to inhibit peptidyl transferase activity rather than by reducing the ability of the ribosome to bind tryptophan
physiological function
-
some of the indigenous posttranscriptional modifications of rRNA can be viewed as intrinsic antibiotic resistance mechanisms. The lack of pseudouridine at position 2504 of 23S rRNA significantly increases the susceptibility of Escherichia coli to peptidyl transferase inhibitors
physiological function
-
recombinant Mycobacterium bovis strain BCG overexpressing a L,D-transpeptidase that is nutrient starved elicits a stronger Th1 type response against virulent MMycobacterium tuberculosis and is at least as protective as parent Mycobacterium bovis strain BCG
physiological function
-
the LdtMt2 protein is required for virulence and resistance to amoxicillin
physiological function
the enzyme catalyzes the formation of 3 -> 3 peptidoglycan cross-links of the cell wall and facilitates resistance against classical beta-lactams
physiological function
the enzyme LdtMt5 is necessary for properly maintaining cell wall integrity
physiological function
-
recombinant Mycobacterium bovis strain BCG overexpressing a L,D-transpeptidase that is nutrient starved elicits a stronger Th1 type response against virulent MMycobacterium tuberculosis and is at least as protective as parent Mycobacterium bovis strain BCG
-
physiological function
-
the LdtMt2 protein is required for virulence and resistance to amoxicillin
-
physiological function
-
the enzyme catalyzes the formation of 3 -> 3 peptidoglycan cross-links of the cell wall and facilitates resistance against classical beta-lactams
-
physiological function
-
the enzyme LdtMt5 is necessary for properly maintaining cell wall integrity
-
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
additional information
-
the enzyme is part of the peptidyl transferase center (PTC), conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control, structure modeling, overview
additional information
the enzyme is part of the peptidyl transferase center (PTC), conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control, structure modeling, overview
additional information
-
the ribosome is capable of polymerizing at a similar rate at least 20 different kinds of amino acids from aminoacyl-tRNA carriers while using just one catalytic site, the peptidyl-transferase center (PTC). The PTC uses an induced-fit mechanism, analysis of published ribosome structures supports the hypothesis that the induced fit eliminates unreactive rotamers predominantly populated for some A-site aminoacyl esters before induction. The hypothesis is fully consistent with the wealth of kinetic data obtained with these substrates. Induction constrains the amino acids into a reactive conformation in a side-chain independent manner. The rationale of the PTC structural organization confers to the ribosome the very unusual ability to handle large as well as small substrates. An induced fit (or conformational change) is identified in the peptidyl-transferase center (PTC) of the ribosome, in which the binding of the 3' acceptor arm of an A-site aminoacyl tRNA triggers a major rearrangement of two ribosome residues, U2506 and U2585, modeling, overview. The room available inside the PTC cavity and its flexibility in the uninduced state leave some conformational freedom to the esterified amino acids. The induced fit orients the aminoacyl ester for nucleophilic attack. PTC structure-function relationship, detailed overview
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
-
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
-
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
-
additional information
-
the enzyme is part of the peptidyl transferase center (PTC)
-
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1978
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Mycobacterium tuberculosis (P9WKV2), Mycobacterium tuberculosis, Mycobacterium tuberculosis CDC 1551 (P9WKV2)
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Tam, B.; Sherf, D.; Cohen, S.; Eisdorfer, S.A.; Perez, M.; Soffer, A.; Vilenchik, D.; Akabayov, S.R.; Wagner, G.; Akabayov, B.
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Escherichia coli
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Lehmann, J.
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