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Enzyme Nomenclature
Information on EC 2.3.2.12 - peptidyltransferase
for references in articles please use BRENDA:EC2.3.2.12
Word Map on EC 2.3.2.12
- 2.3.2.12
- rrnas
- puromycin
-
nascent
- aminoacyl-trnas
-
p-site
-
exit
-
tunnel
-
macrolide
- erythromycin
-
decoding
-
aminoacylated
-
stall
-
oxazolidinones
-
anticodon
-
cryo-electron
- marismortui
- clindamycin
-
transpeptidation
- anisomycin
- polyu
-
protuberance
- clarithromycin
-
lincosamide
- trnaphe
- linezolid
-
haloarcula
-
polyphenylalanine
-
ribozyme
-
peptide-bond
-
streptogramins
-
penicillin-binding
-
blasticidin
-
fmet-trna
- pseudouridine
- medicine
- dbpa
- tylosin
- phenylalanyl-trna
- spiramycin
- phe-trna
-
aa-trna
-
virginiamycin
-
ketolide
-
ribosome-bound
-
phe-trnaphe
- thiostrepton
- telithromycin
-
polyu-directed
-
polyphe
-
photoincorporation
- lincomycin
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The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
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EC NUMBER 
COMMENTARY 
2.3.2.12
-
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RECOMMENDED NAME
GeneOntology No.
peptidyltransferase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
peptidyl-tRNA1 + aminoacyl-tRNA2 = tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
peptidyl-tRNA1 + aminoacyl-tRNA2 = tRNA1 + peptidyl(aminoacyl-tRNA2)
The peptidyl transferase reaction involves aminolysis by the alpha-amino group of the A-site aminoacyl-tRNA of the ester bond that links the nascent peptide to the 3'-hydroxyl of the 3'-terminal ribose of the P-site tRNA. The termination reaction involves the transfer of the peptidyl moiety of P-site located peptidyl-tRNA to a water molecule, in the course of the reaction the nucleophilic attack of an activated water molecule in the peptidyl transferase center acceptor site onto the carbonyl carbon of the peptidyl-tRNA ester leads to formation of a tetrahedral intermediate, a proton from the water is subsequently transferred to the 2'(3')-hydroxyl of the 3'-terminal adenosine of peptidyl-tRNA, breaking the ester bond between the peptide and tRNA
-
peptidyl-tRNA1 + aminoacyl-tRNA2 = tRNA1 + peptidyl(aminoacyl-tRNA2)
The peptidyl transferase reaction involves aminolysis by the alpha-amino group of the A-site aminoacyl-tRNA of the ester bond that links the nascent peptide to the 3'-hydroxyl of the 3'-terminal ribose of the P-site tRNA. The termination reaction involves the transfer of the peptidyl moiety of P-site located peptidyl-tRNA to a water molecule, in the course of the reaction the nucleophilic attack of an activated water molecule in the peptidyl transferase center acceptor site onto the carbonyl carbon of the peptidyl-tRNA ester leads to formation of a tetrahedral intermediate, a proton from the water is subsequently transferred to the 2'(3')-hydroxyl of the 3'-terminal adenosine of peptidyl-tRNA, breaking the ester bond between the peptide and tRNA
-
peptidyl-tRNA1 + aminoacyl-tRNA2 = tRNA1 + peptidyl(aminoacyl-tRNA2)
The peptidyl transferase reaction involves aminolysis by the alpha-amino group of the A-site aminoacyl-tRNA of the ester bond that links the nascent peptide to the 3'-hydroxyl of the 3'-terminal ribose of the P-site tRNA. The termination reaction involves the transfer of the peptidyl moiety of P-site located peptidyl-tRNA to a water molecule, in the course of the reaction the nucleophilic attack of an activated water molecule in the peptidyl transferase center acceptor site onto the carbonyl carbon of the peptidyl-tRNA ester leads to formation of a tetrahedral intermediate, a proton from the water is subsequently transferred to the 2'(3')-hydroxyl of the 3'-terminal adenosine of peptidyl-tRNA, breaking the ester bond between the peptide and tRNA
-
peptidyl-tRNA1 + aminoacyl-tRNA2 = tRNA1 + peptidyl(aminoacyl-tRNA2)
The peptidyl transferase reaction involves aminolysis by the alpha-amino group of the A-site aminoacyl-tRNA of the ester bond that links the nascent peptide to the 3' hydroxyl of the 3' terminal ribose of the P-site tRNA. The termination reaction involves the transfer of the peptidyl moiety of P-site located peptidyl-tRNA to a water molecule, in the course of the reaction the nucleophilic attack of an activated water molecule in the peptidyl transferase center acceptor site onto the carbonyl carbon of the peptidyl-tRNA ester leads to formation of a tetrahedral intermediate, a proton from the water is subsequently transferred to the 2'(3')-hydroxyl of the 3'-terminal adenosine of peptidyl-tRNA, breaking the ester bond between the peptide and tRNA
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
aminoacyl group transfer
-
-
-
-
peptidyl group transfer
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
peptidyl-tRNA:aminoacyl-tRNA N-peptidyltransferase
The enzyme is a ribozyme. Two non-equivlant ribonucleoprotein subunits operate in non-concerted fashion in peptide elongation. The small subunit forms the mRNA-binding machinery and decoding center, the large subunit performs the main ribosomal catalytic function in the peptidyl-transferase center.
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CAS REGISTRY NUMBER
COMMENTARY
9059-29-4
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
487796, 487803, 487805, 487815, 658114, 660033, 671368, 672030, 673179, 673338, 674198, 675409, 698614, 699543, 718466, 719503, 720610, 720898, 736089, 736368, 737231
-
-
wild type strain 2D-J809, strain 2A-J809 lacking the two genes encoding L24, strain L1726 lacking the single gene encoding L39, strain L1725 lacking the genes for both proteins L24 and L39
-
-
wild type strain YKS99-2A, strain YKS99-2C missing the protein L41, the two genes RPL41A and RPL41B
-
-
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
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
-
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; 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
-
metabolism
-
the peptidoglycans of the rough and smooth morphotypes contain predominantly 3->3 cross-links generated by L,D-transpeptidases
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
-
the LdtMt2 protein is required for virulence and resistance to amoxicillin
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 enzyme LdtMt5 is necessary for properly maintaining cell wall integrity
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
-
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 enzyme catalyzes the formation of 3 -> 3 peptidoglycan cross-links of the cell wall and facilitates resistance against classical beta-lactams; the enzyme LdtMt5 is necessary for properly maintaining cell wall integrity; the LdtMt2 protein is required for virulence and resistance to amoxicillin
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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 + ?
?
-
-
-
-
-
formylmethionyl-tRNA + alpha-hydroxy-puromycin
tRNA + formylmethionyl-alpha-hydroxy-puromycin
-
ester linkage
-
?
GlcNAc-MurNGlyc-L-Ala1-D-iGln2-meso-DapNH23-D-Ala4 + D-methionine
GlcNAc-MurNGlyc-L-Ala1-D-iGln2-meso-DapNH23-D-Met4 + D-alanine
-
-
-
-
?
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
-
-
-
-
?
N-AcMet-tRNA + puromycin
tRNA + N-AcMet-puromycin
-
-
-
?
polyphenylalanyl-tRNA + puromycin
tRNA + polyphenylalanyl-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-polyU-70S 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-polyU-80S ribosome complex
-
?
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
-
fragment reaction
-
?
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
-
fragment reaction
-
?
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
-
fragment reaction
-
?
formylmethionyl-tRNA + puromycin
tRNA + formylmethionyl-puromycin
-
-
-
?
formylmethionyl-tRNA + puromycin
tRNA + formylmethionyl-puromycin
-
formylmethionyl-tRNA-AUG-70S ribosome complex
-
?
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)
Mycobacterium smegmatis mc(2)155 / ATCC 700084
-
-
-
-
?
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
-
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
?
-
-
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
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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)
Mycobacterium smegmatis mc(2)155 / ATCC 700084
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
O53223
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
P9WKV2
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
O53223
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
P9WKV2
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
-
the velocity of the reaction measured at limiting concentrations of Met-tRNA and saturating puromycin increases with Mg2+ concentration up to about 100 mM
Mg2+
-
the ribosomal peptidyl transferase center is supported by a framework of magnesium microclusters. Common features of Mg2+-microclusters include two paired Mg2+ ions that are chelated by a common bridging phosphate group in the form Mg2+(a)-(O1P-PO2P)-Mg2+(b). This bridging phosphate is part of a 10-membered chelation ring in the form Mg2+(a)-(OP-P-O5'-C5'-C4'-C3'-O3'-P-OP)-Mg2+(a). The two phosphate groups of this 10-membered ring are contributed by adjacent residues along the RNA backbone. Both Mg2+ ions are octahedrally coordinated, but are substantially dehydrated by interactions with additional RNA phosphate groups. The Mg2+-microclusters in the large subunit appear to be highly conserved over evolution
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
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
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
additional information
-
the peptidyl transferase center is not inhibited by D-arginine
-
Amicetin
-
complete inhibition with AcPhe-tRNA as donor, with polylysyl-tRNA as donor less active
anisomycin
-
inhibition of formation of AcPhe-puromycin catalyzed by rabbit reticulocyte ribosomes
blasticidin S
-
inhibition of formation of Ac-Phe-puromycin catalyzed by rabbit reticulocyte ribosomes
Chloramphenicol
-
competitive inhibition with acetylphenylalanyl-tRNA-polyU-ribosome complex, newly formed complex is inactive towards puromycin
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
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
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
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
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
NH4+
-
combination of NH4+ ions with spermine produces an additive activity increase
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0102
AcPhe-tRNA
-
strain YKS99-2C missing the protein L41, the two genes RPL41A and RPL41B
-
0.0115
AcPhe-tRNA
-
strain 2A-J809 lacking the two genes encoding L24
-
0.0178
AcPhe-tRNA
-
triple mutant strain L1725 lacking the proteins L24 and L39
-
0.0508
AcPhe-tRNA
-
strain L1729 lacking the single gene encoding L39
-
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
30
37
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
additionally factors washable from ribosomes
-
-
487797, 487798, 487800, 487802, 487805, 487807, 487808, 487815, 719503, 720610, 720898, 736089, 737231
-
50S subunit, wild type ribosomes, ribosomes with site-directed mutated residues: A2451, G2447
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
49700
-
x * 49700, LtdC, calculated from amino acid sequence; x * 49700, LtdG, calculated from amino acid sequence
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
x * 28500, LtdA, calculated from amino acid sequence; x * 38100, LtdE, calculated from amino acid sequence; x * 44000, LtdB, calculated from amino acid sequence; x * 46200, LtdF, calculated from amino acid sequence; x * 49700, LtdC, calculated from amino acid sequence; x * 49700, LtdG, calculated from amino acid sequence
?
Mycobacterium smegmatis mc(2)155 / ATCC 700084
-
x * 28500, LtdA, calculated from amino acid sequence; x * 38100, LtdE, calculated from amino acid sequence; x * 44000, LtdB, calculated from amino acid sequence; x * 46200, LtdF, calculated from amino acid sequence; x * 49700, LtdC, calculated from amino acid sequence
-
?
-
x * 27600, LtdA, calculated from amino acid sequence; x * 29800, LtdD, calculated from amino acid sequence; x * 40200, LtdE, calculated from amino acid sequence; x * 44900, LtdB, calculated from amino acid sequence; x * 49600, LtdC, calculated from amino acid sequence
?
-
x * 27600, LtdA, calculated from amino acid sequence; x * 29800, LtdD, calculated from amino acid sequence; x * 40200, LtdE, calculated from amino acid sequence; x * 44900, LtdB, calculated from amino acid sequence; x * 49600, LtdC, calculated from amino acid sequence
-
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
structure of the inhibitor linezolid bound to the 50S ribosomal subunit. 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
-
structures at 3.5 A and 3.55 A resolution of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and postpeptidyl transfer states, respectively. The peptidyl transfer center is very similar between the 50S subunit and the intact ribosome. Structures reveal interactions between ribosomal proteins L16 and L27 and the tRNA substrates
-
hanging drop vapor diffusion method, using 85 mM sodium citrate, pH 5.6, 25.5% (w/v) polyethylene glycol 4000, 170 mM ammonium acetate, and 15% (v/v) glycerol
sitting drop vapor diffusion method, using 0.2 M ammonium sulfate, 0.1 M bis-Tris-HCl pH 6.5, 25% (w/v) PEG 3350
-
cross-crystal averaging over two crystal structures of the 70S ribosome in the same functional state. The structure of the peptidyl transferase center is the same in the functionally equivalent 70S ribosome and the 50S subunit
-
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
the A2453-C2499 wobble base pair in Escherichia coli 23S ribosomal RNA is responsible for pH sensitivity of the peptidyltransferase active site conformation
660033
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ni-NTA resin column chromatography and Superdex 200 gel filtration
-
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the enzyme is upregulated in response to Cpx envelope stress response-inducing conditions
-
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A2451U
-
with puromycin as an acceptor substrate, the catalytic rate of the mutant enzyme decreases about 150fold relative to wild type enzyme
A2451U
-
the base identity at this highly conserved residue is not absolutely critical for peptide bond synthesis
additional information
additional information
-
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
additional information
-
lack of pseudouridine at position 2504 of 23S rRNA significantly increases the susceptibility of Escherichia coli to peptidyl transferase inhibitors
additional information
-
the lethal mutation UU2492-3C affects the function of ribosomal peptidyl transferase center. Binding of Phe-tRNAPhe to the A site of ribosomes with mutation UU2492-3C is much lower comparing to wild type ribosomes (27% and 77%, respectively). Mutant ribosomes are not able to catalyze peptidyl transfer reaction with puromycin as the A-site substrate
additional information
-
the antibiotic resistance mutation G2482A enhances conformational fluctuation at the antibiotic binding site, weakens the hydrogen-bonding network, and increases flexibility at the 50S peptidyl transferase center
additional information
-
introduction of individual 23S rRNA mutations associated with pleuromutilin resistance at positions 2055, 2447, 2504 and 2572, Escherichia coli numbering, into a Mycobacterium smegmatis strain with a single rRNA operon. The single mutations each confer a significant and similar degree of valnemulin resistance and those at 2447 and 2504 also confer cross-resistance to other antibiotics that bind to the peptidyl transfer center. The introduced mutations cause structural perturbations at the peptidyl transfer center and reduce binding of pleuromutilin antibiotics
additional information
-
single mutations at positions 2032, 2453, and 2499 to human cytosolic base identity do not confer significantly reduced susceptibility to linezolid. The largest decrease in linezolid susceptibility is observed with the G2576U mutation
additional information
-
mutant DELTAldtC is hypersusceptible to imipenem
additional information
Mycobacterium smegmatis mc(2)155 / ATCC 700084
-
mutant DELTAldtC is hypersusceptible to imipenem
-
additional information
-
single mutations at positions 2032, 2453, and 2499 to human cytosolic base identity do not confer significantly reduced susceptibility to linezolid. The largest decrease in linezolid susceptibility is observed with the G2576U mutation
-
additional information
-
three bases in the catalytic core of the peptidyltransferase center - A2819-20 (A2450 and A2451) and U2875 (U2506) - are hyperprotected from 1M7 reagent but not dimethylsulfate modification in U2861A ribosomes
additional information
-
mutations at base A2451 lead to strongly decreased enzyme activity
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
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LINKS TO OTHER DATABASES (specific for EC-Number 2.3.2.12)
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