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Information on EC 2.3.2.12 - peptidyltransferase
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2.3.2.12 peptidyltransferaseIUBMB Comments
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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Word Map
- 2.3.2.12
- rrnas
- puromycin
- aminoacyl-trnas
-
tunnel
-
p-site
-
exit
-
macrolide
-
decoding
-
aminoacylated
- erythromycin
-
stall
-
ribosome-bound
- clindamycin
-
penicillin-binding
-
cryo-electron
-
haloarcula
-
protuberance
-
peptide-bond
- linezolid
-
transpeptidation
-
lincosamide
- clarithromycin
-
streptogramins
- marismortui
- trnaphe
-
polyphenylalanine
-
oxazolidinones
- polyu
-
ribozyme
-
anticodon
-
virginiamycin
-
polyu-directed
-
phe-trnaphe
- spiramycin
- dbpa
- phe-trna
-
polyphe
- pseudouridine
-
photoincorporation
- tylosin
-
blasticidin
- lincomycin
- phenylalanyl-trna
- carbapenems
-
aa-trnas
- medicine
- telithromycin
-
fmet-trna
-
ketolide
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
peptidyl transferase, peptidyltransferase, ribosomal peptidyl transferase, ribosomal peptidyltransferase, ldtmt2, ribosomal protein l27, ptase, peptidoglycan transpeptidase, ldtfm, ldtmt5, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
L,D-transpeptidase
L,D-transpeptidase 2
LD-transpeptidase
LDT
LdtMt2
LdtMt5
peptidyl transferase
PT
PTC
ribosomal peptidyl transferase
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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
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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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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
acetylphenylalanyl-tRNA + puromycin
acetylphenylalanyl-puromycin + tRNA
-
-
-
?
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)
-
-
?
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)
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
-
-
?
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 SUBSTRATE
NATURAL 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
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)
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
-
-
-
?
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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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INHIBITOR
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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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
-
-
brenda
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
-
-
brenda
wild type strain YKS99-2A, strain YKS99-2C missing the protein L41, the two genes RPL41A and RPL41B
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
-
487797, 487798, 487800, 487802, 487805, 487807, 487808, 487815, 719503, 720610, 720898, 736089, 737231
brenda
-
additionally factors washable from ribosomes
brenda
-
50S subunit, wild type ribosomes, ribosomes with site-directed mutated residues: A2451, G2447
brenda
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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
-
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
Mycobacteroides abscessus CIP104536T
-
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
Mycobacterium tuberculosis variant bovis BCG Copenhagen
-
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
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). Q9VWT3_DROME
579
1
62872
TrEMBL
Secretory Pathway (Reliability: 1)
Q9XZS5_DROME
571
1
62469
TrEMBL
Secretory Pathway (Reliability: 1)
D5A7L0_DROME
501
0
55505
TrEMBL
other Location (Reliability: 3)
A8JV19_DROME
732
1
78338
TrEMBL
other Location (Reliability: 2)
Q9VYR2_DROME
592
1
65231
TrEMBL
Secretory Pathway (Reliability: 1)
M9NFP5_DROME
585
1
64027
TrEMBL
Secretory Pathway (Reliability: 4)
Q9VXA5_DROME
777
1
83553
TrEMBL
other Location (Reliability: 3)
A8JV25_DROME
687
1
74297
TrEMBL
other Location (Reliability: 3)
Q7KUX2_DROME
822
1
87594
TrEMBL
other Location (Reliability: 2)
M9PHT3_DROME
491
0
53479
TrEMBL
other Location (Reliability: 4)
LDT2_MYCTO
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
408
0
43366
Swiss-Prot
-
LDT5_MYCTO
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
451
0
47891
Swiss-Prot
-
A0A0H2UNQ9_STRPN
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
279
0
31705
TrEMBL
-
Q3Y185_ENTFD
Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
466
0
52056
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
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
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
x * 28500, LtdA, calculated from amino acid sequence
?
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
x * 38100, LtdE, calculated from amino acid sequence
?
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
x * 44000, LtdB, calculated from amino acid sequence
?
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
x * 46200, LtdF, calculated from amino acid sequence
?
Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
-
x * 49700, 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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PROTEIN VARIANTS
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
Mycolicibacterium 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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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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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kalpaxis, D.L.; Drainas D.
Inhibitory effect of spermine on ribosomal peptidyltransferase
Arch. Biochem. Biophys.
300
629-634
1993
Escherichia coli
brenda
Traut, R.R.; Monro, R.E.
The puromycin reaction and its relation to protein synthesis
J. Mol. Biol.
10
63-72
1964
Escherichia coli
brenda
Rychlik, I.
Release of lysine peptides by puromycin from polylysyl-transfer ribonucleic acid in the presence of ribosomes
Biochim. Biophys. Acta
114
425-427
1966
Escherichia coli
brenda
Cerna, J.; Rychlik, I.; Lichtenthaler, F.W.
The effect of the aminoacyl-4-aminohexosyl-cytosine group of antibiotics on ribosomal peptidyl transferase
FEBS Lett.
30
147-150
1973
Escherichia coli
brenda
Thompson, H.A.; Moldave, K.
Characterization of the peptidyltransferase reaction catalyzed by rat liver 60S ribosomal subunits
Biochemistry
13
1348-1353
1974
Rattus norvegicus
brenda
Fahnestock, S.; Neumann, H.; Rich, A.
Assay of ester and polyester formation by the ribosomal peptidyltransferase
Methods Enzymol.
30 F
489-497
1974
Escherichia coli
-
brenda
Lichtenthaler, F.W.; Cerna, J.; Rychlik, I.
The effect of oxamicetin and some amicetin analogs on ribosomal peptidyl transferase
FEBS Lett.
53
184-187
1975
Escherichia coli
brenda
Spirin, A.S.; Asatryan, L.S.
The effect of ribosomal peptidyl-transferase inhibitors is antagonized by elongation factor G with GTP
FEBS Lett.
70
101-104
1976
Escherichia coli, Escherichia coli MRE 600
brenda
Bhuta, P.; Zemlicka, J.
Inhibition of ribosomal peptidyltransferase with cytidyl-3 leads to 5-[2(3)-O-L-phenylalanyl]-L-adenosine
Biochem. Biophys. Res. Commun.
83
414-420
1978
Escherichia coli
brenda
Streltsov, S.; Kosenjuk, A.; Kukhanova, M.; Krayevsky, A.; Gottikh, B.
Kinetic constants for model substrates of peptidyltransferase donor site of Escherichia coli ribosomes
FEBS Lett.
104
279-283
1979
Escherichia coli, Escherichia coli MRE 600
brenda
Cerna, J.; Rychlik, I.
Phenylboric acids - A new group of peptidyl transferase inhibitors
FEBS Lett.
119
342-348
1980
Escherichia coli
-
brenda
Chladek, S.; Bhuta, P.
Inhibition of the peptidyltransferase acceptor site by 2(3)-O-cycloleucyl- and alpha-aminoisobutyryl derivatives of cytidylyl-(3-5)adenosine
Biochim. Biophys. Acta
696
212-217
1982
Escherichia coli, Escherichia coli MRE 600
brenda
Kalpaxis, D.L.; Theocharis, D.A.; Coutsogeorgopoulos, C.
Kinetic studies on ribosomal peptidyltransferase. The behaviour of the inhibitor blasticidin S
Eur. J. Biochem.
154
267-271
1986
Escherichia coli
brenda
Drainas D.; Kalpaxis, D.L.; Coutsogeorgopoulos, C.
Inhibition of ribosomal peptidyltransferase by chloramphenicol. Kinetic studies
Eur. J. Biochem.
164
53-58
1987
Escherichia coli
brenda
Synetos, D.; Coutsogeorgopoulos, C.
Studies on the catalytic rate constant of ribosomal peptidyltransferase
Biochim. Biophys. Acta
923
275-285
1987
Escherichia coli
brenda
Michelinaki, M.; Mamos, P.; Coutsogeorgopoulos, C.; Kalpaxis, D.L.
Aminoacyl and peptidyl analogs of chloramphenicol as slow-binding inhibitors of ribosomal peptidyltransferase: a new approach for evaluating their potency
Mol. Pharmacol.
51
139-146
1997
Escherichia coli
brenda
Ioannou, M.; Coutsogeorgopoulos, C.; Drainas, D.
Determination of eukaryotic peptidyltransferase activity by pseudo-first-order kinetic analysis
Anal. Biochem.
247
115-122
1997
Oryctolagus cuniculus
brenda
Michelinaki, M.; Spanos, A.; Coutsogeorgopoulos, C.; Kalpaxis, D.L.
New aspects on the kinetics of activation of ribosomal peptidyltransferase-catalyzed peptide bond formation by monovalent ions and spermine
Biochim. Biophys. Acta
1342
182-190
1997
Escherichia coli
brenda
Ioannou, M.; Coutsogeorgopoulos, C.
Kinetic studies on the activation of eukaryotic peptidyltransferase by potassium
Arch. Biochem. Biophys.
345
325-331
1997
Oryctolagus cuniculus
brenda
Ioannou, M.; Coutsogeorgopoulos, C.; Synetos, D.
Kinetics of inhibition of rabbit reticulocyte peptidyltransferase by anisomycin and sparsomycin
Mol. Pharmacol.
53
1089-1096
1998
Oryctolagus cuniculus
brenda
Karahalios, P.; Mamos, P.; Karigiannis, G.; Kalpaxis, D.L.
Structure/function correlation of spermine-analog-induced modulation of peptidyltransferase activity
Eur. J. Biochem.
258
437-444
1998
Escherichia coli
brenda
Thompson, J.; Kim, D.F.; O'Connor, M.; Lieberman, K.R.; Bayfield, M.A.; Gregory, S.T.; Green, R.; Noller, H.F.; Dahlberg, A.E.
Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit
Proc. Natl. Acad. Sci. USA
98
9002-9007
2001
Geobacillus stearothermophilus
brenda
Dresios, J.; Panopoulos, P.; Frantziou, C.P.; Synetos, D.
Yeast Ribosomal Protein Deletion Mutants Possess Altered Peptidyltransferase Activity and Different Sensitivity to Cycloheximide
Biochemistry
40
8101-8108
2001
Saccharomyces cerevisiae
brenda
Dresios, J.; Panopoulos, P.; Suzuki, K.; Synetos, D.
A dispensable yeast ribosomal protein optimizes peptidyltransferase activity and affects translocation
J. Biol. Chem.
278
3314-3322
2003
Saccharomyces cerevisiae
brenda
Seila, A.C.; Okuda, K.; Nunez, S.; Seila, A.F.; Strobel, S.A.
Kinetic isotope effect analysis of the ribosomal peptidyl transferase reaction
Biochemistry
44
4018-4027
2005
Escherichia coli
brenda
Bayfield, M.A.; Thompson, J.; Dahlberg, A.E.
The A2453-C2499 wobble base pair in Escherichia coli 23S ribosomal RNA is responsible for pH sensitivity of the peptidyltransferase active site conformation
Nucleic Acids Res.
32
5512-5518
2004
Escherichia coli
brenda
Moore, P.B.; Steitz, T.A.
After the ribosome structures: How does peptidyl transferase work?
RNA
9
155-159
2003
Haloarcula marismortui
brenda
Curtis, N.A.; Brown, C.; Boxall, M.; Boulton, M.G.
Modified peptidoglycan transpeptidase activity in a carbenicillin-resistant mutant of Pseudomonas aeruginosa 18s
Antimicrob. Agents Chemother.
14
246-251
1978
Pseudomonas aeruginosa
brenda
Long, K.S.; Hansen, L.H.; Jakobsen, L.; Vester, B.
Interaction of pleuromutilin derivatives with the ribosomal peptidyl transferase center
Antimicrob. Agents Chemother.
50
1458-1462
2006
Escherichia coli
brenda
Okuda, K.; Seila, A.C.; Strobel, S.A.
Uncovering the enzymatic pKa of the ribosomal peptidyl transferase reaction utilizing a fluorinated puromycin derivative
Biochemistry
44
6675-6684
2005
Escherichia coli
brenda
Polacek, N.; Mankin, A.S.
The ribosomal peptidyl transferase center: structure, function, evolution, inhibition
Crit. Rev. Biochem. Mol. Biol.
40
285-311
2005
Deinococcus radiodurans, Escherichia coli, Haloarcula marismortui, Mycolicibacterium smegmatis
brenda
Wohlgemuth, I.; Beringer, M.; Rodnina, M.V.
Rapid peptide bond formation on isolated 50S ribosomal subunits
EMBO Rep.
7
699-703
2006
Escherichia coli
brenda
Erlacher, M.D.; Lang, K.; Wotzel, B.; Rieder, R.; Micura, R.; Polacek, N.
Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2-OH at A2451 of 23S rRNA
J. Am. Chem. Soc.
128
4453-4459
2006
Escherichia coli
brenda
Feinberg, J.S.; Joseph, S.
A conserved base-pair between tRNA and 23 S rRNA in the peptidyl transferase center is important for peptide release
J. Mol. Biol.
364
1010-1020
2006
Escherichia coli
brenda
Schmeing, T.M.; Huang, K.S.; Strobel, S.A.; Steitz, T.A.
An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA
Nature
438
520-524
2005
Haloarcula marismortui
brenda
Erlacher, M.D.; Lang, K.; Shankaran, N.; Wotzel, B.; Huettenhofer, A.; Micura, R.; Mankin, A.S.; Polacek, N.
Chemical engineering of the peptidyl transferase center reveals an important role of the 2-hydroxyl group of A2451
Nucleic Acids Res.
33
1618-1627
2005
Thermus aquaticus
brenda
Rakauskaite, R.; Dinman, J.D.
rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance
Nucleic Acids Res.
36
1497-1507
2008
Saccharomyces cerevisiae
brenda
Rodriguez-Correa, D.; Dahlberg, A.E.
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus
RNA
14
2314-2318
2008
Thermus thermophilus
brenda
Miller, K.; Dunsmore, C.J.; Fishwick, C.W.; Chopra, I.
Linezolid and tiamulin cross-resistance in Staphylococcus aureus mediated by point mutations in the peptidyl transferase center
Antimicrob. Agents Chemother.
52
1737-1742
2008
Thermus thermophilus
brenda
Yang, R.; Cruz-Vera, L.R.; Yanofsky, C.
23S rRNA nucleotides in the peptidyl transferase center are essential for tryptophanase operon induction
J. Bacteriol.
191
3445-3450
2009
Escherichia coli
brenda
Toh, S.M.; Mankin, A.S.
An indigenous posttranscriptional modification in the ribosomal peptidyl transferase center confers resistance to an array of protein synthesis inhibitors
J. Mol. Biol.
380
593-597
2008
Escherichia coli
brenda
Ge, X.; Roux, B.
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials
J. Mol. Recognit.
23
128-141
2010
Haloarcula marismortui
brenda
Long, K.S.; Poehlsgaard, J.; Hansen, L.H.; Hobbie, S.N.; Boettger, E.C.; Vester, B.
Single 23S rRNA mutations at the ribosomal peptidyl transferase centre confer resistance to valnemulin and other antibiotics in Mycobacterium smegmatis by perturbation of the drug binding pocket
Mol. Microbiol.
71
1218-1227
2009
Mycolicibacterium smegmatis
brenda
Voorhees, R.M.; Weixlbaumer, A.; Loakes, D.; Kelley, A.C.; Ramakrishnan, V.
Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome
Nat. Struct. Mol. Biol.
16
528-533
2009
Haloarcula marismortui
brenda
Hsiao, C.; Williams, L.D.
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center
Nucleic Acids Res.
37
3134-3142
2009
Haloarcula marismortui
brenda
Wilson, D.N.; Schluenzen, F.; Harms, J.M.; Starosta, A.L.; Connell, S.R.; Fucini, P.
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
Proc. Natl. Acad. Sci. USA
105
13339-13344
2008
Deinococcus radiodurans
brenda
Simonovic, M.; Steitz, T.A.
Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit
Proc. Natl. Acad. Sci. USA
105
500-505
2008
Thermus thermophilus
brenda
McCusker, K.P.; Fujimori, D.G.
The chemistry of peptidyltransferase center-targeted antibiotics: enzymatic resistance and approaches to countering resistance
ACS Chem. Biol.
7
64-72
2012
Escherichia coli
brenda
Long, K.S.; Munck, C.; Andersen, T.M.; Schaub, M.A.; Hobbie, S.N.; Boettger, E.C.; Vester, B.
Mutations in 23S rRNA at the peptidyl transferase center and their relationship to linezolid binding and cross-resistance
Antimicrob. Agents Chemother.
54
4705-4713
2010
Mycolicibacterium smegmatis, Mycolicibacterium smegmatis SZ558
brenda
Burakovsky, D.E.; Sergiev, P.V.; Steblyanko, M.A.; Konevega, A.L.; Bogdanov, A.A.; Dontsova, O.A.
The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of Escherichia coli ribosome
FEBS Lett.
585
3073-3078
2011
Escherichia coli
brenda
Wang, Y.; Shen, J.; Schroeder, S.
Nucleotide dynamics at the A-site cleft in the peptidyltransferase center of H. marismortui 50S ribosomal subunits
J. Phys. Chem. Lett.
3
1007-1010
2012
Haloarcula marismortui
brenda
Ramu, H.; Vazquez-Laslop, N.; Klepacki, D.; Dai, Q.; Piccirilli, J.; Micura, R.; Mankin, A.S.
Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center
Mol. Cell
41
321-330
2011
Neurospora crassa
brenda
Chirkova, A.; Erlacher, M.D.; Clementi, N.; Zywicki, M.; Aigner, M.; Polacek, N.
The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center
Nucleic Acids Res.
38
4844-4855
2010
Thermus aquaticus
brenda
Kostopoulou, O.; Kourelis, T.; Mamos, P.; Magoulas, G.; Kalpaxis, D.
Insights into the chloramphenicol inhibition effect on peptidyl transferase activity, using two new analogs of the drug
Open Enz. Inhib. J.
4
1-10
2011
Escherichia coli
-
brenda
Dunkle, J.A.; Xiong, L.; Mankin, A.S.; Cate, J.H.
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action
Proc. Natl. Acad. Sci. USA
107
17152-17157
2010
Escherichia coli
brenda
Rakauskaite, R.; Dinman, J.D.
Mutations of highly conserved bases in the peptidyltransferase center induce compensatory rearrangements in yeast ribosomes
RNA
17
855-864
2011
Saccharomyces cerevisiae
brenda
Lecoq, L.; Dubee, V.; Triboulet, S.; Bougault, C.; Hugonnet, J.E.; Arthur, M.; Simorre, J.P.
Structure of Enterococcus faecium L,D-transpeptidase acylated by ertapenem provides insight into the inactivation mechanism
ACS Chem. Biol.
8
1140-1146
2013
Enterococcus faecium
brenda
Boeth, D.; Steiner, E.M.; Stadler, D.; Lindqvist, Y.; Schnell, R.; Schneider, G.
Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis
Acta Crystallogr. Sect. D
69
432-441
2013
Mycobacterium tuberculosis (O53223), Mycobacterium tuberculosis, Mycobacterium tuberculosis CDC 1551 (O53223)
brenda
Cordillot, M.; Dubee, V.; Triboulet, S.; Dubost, L.; Marie, A.; Hugonnet, J.E.; Arthur, M.; Mainardi, J.L.
In vitro cross-linking of Mycobacterium tuberculosis peptidoglycan by L,D-transpeptidases and inactivation of these enzymes by carbapenems
Antimicrob. Agents Chemother.
57
5940-5945
2013
Mycobacterium tuberculosis
brenda
Silva, J.R.; Govender, T.; Maguire, G.E.; Kruger, H.G.; Lameira, J.; Roitberg, A.E.; Alves, C.N.
Simulating the inhibition reaction of Mycobacterium tuberculosis L,D-transpeptidase 2 by carbapenems
Chem. Commun. (Camb.)
51
12560-12562
2015
Mycobacterium tuberculosis
brenda
Yanshina, D.D.; Bulygin, K.N.; Malygin, A.A.; Karpova, G.G.
Hydroxylated histidine of human ribosomal protein uL2 is involved in maintaining the local structure of 28S rRNA in the ribosomal peptidyl transferase center
FEBS J.
282
1554-1566
2015
Escherichia coli
brenda
Farias, S.T.; Rego, T.G.; Jose, M.V.
Origin and evolution of the Peptidyl Transferase Center from proto-tRNAs
FEBS open bio
4
175-178
2014
Thermus thermophilus
brenda
Bernal-Cabas, M.; Ayala, J.A.; Raivio, T.L.
The Cpx envelope stress response modifies peptidoglycan cross-linking via the L,D-transpeptidase LdtD and the novel protein YgaU
J. Bacteriol.
197
603-614
2015
Escherichia coli
brenda
Brammer Basta, L.A.; Ghosh, A.; Pan, Y.; Jakoncic, J.; Lloyd, E.P.; Townsend, C.A.; Lamichhane, G.; Bianchet, M.A.
Loss of a functionally and structurally distinct LD-transpeptidase, LdtMt5, compromises cell wall integrity in Mycobacterium tuberculosis
J. Biol. Chem.
290
25670-25685
2015
Mycobacterium tuberculosis (P9WKV2), Mycobacterium tuberculosis, Mycobacterium tuberculosis CDC 1551 (P9WKV2)
brenda
Silva, J.R.; Roitberg, A.E.; Alves, C.N.
Catalytic mechanism of L,D-transpeptidase 2 from Mycobacterium tuberculosis described by a computational approach: insights for the design of new antibiotics drugs
J. Chem. Inf. Model.
54
2402-2410
2014
Mycobacterium tuberculosis (O53223), Mycobacterium tuberculosis, Mycobacterium tuberculosis CDC 1551 (O53223)
brenda
Sanders, A.N.; Wright, L.F.; Pavelka, M.S.
Genetic characterization of mycobacterial L,D-transpeptidases
Microbiology
160
1795-1806
2014
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv, Mycolicibacterium smegmatis, Mycolicibacterium smegmatis mc(2)155 / ATCC 700084
brenda
Triboulet, S.; Bougault, C.M.; Laguri, C.; Hugonnet, J.E.; Arthur, M.; Simorre, J.P.
Acyl acceptor recognition by Enterococcus faecium L,D-transpeptidase Ldtfm
Mol. Microbiol.
98
90-100
2015
Enterococcus faecium
brenda
Maracci, C.; Wohlgemuth, I.; Rodnina, M.V.
Activities of the peptidyl transferase center of ribosomes lacking protein L27
RNA
21
2047-2052
2015
Escherichia coli, Escherichia coli IW312
brenda
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