Information on EC 2.3.2.12 - peptidyltransferase

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The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota

EC NUMBER
COMMENTARY hide
2.3.2.12
-
RECOMMENDED NAME
GeneOntology No.
peptidyltransferase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
peptidyl-tRNA1 + aminoacyl-tRNA2 = tRNA1 + peptidyl(aminoacyl-tRNA2)
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
aminoacyl group transfer
-
-
-
-
peptidyl group transfer
-
-
-
-
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.
CAS REGISTRY NUMBER
COMMENTARY hide
9059-29-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
strains 18sH Con- and 18s SAI-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2'(3')-O-(N-formylmethionyl)-adenosine-5'-phosphate + CACCA-Phe
?
show the reaction diagram
-
-
-
-
?
AcPhe-tRNA + pCpCp-puromycin
tRNA + AcPhe-pCpCp-puromycin
show the reaction diagram
-
-
-
-
?
AcPhe-tRNA + puromycin
tRNA + AcPhe-puromycin
show the reaction diagram
CACCA-AcLeu + puromycin
CACCA + AcLeu-puromycin
show the reaction diagram
cytidylyl-(3',5'-phosphoryl)-3'-amino-3'-deoxy-3'-L-beta,beta-difluorophenylalanyl-N6,N6-dimethyladenosine + ?
?
show the reaction diagram
-
-
-
-
?
cytidylyl-(3',5'-phosphoryl)-3'-amino-3'-deoxy-3'-L-phenylalanyl-N6,N6-dimethyladenosine + ?
?
show the reaction diagram
-
-
-
-
-
formyl-Met-tRNA + puromycin
tRNA + formyl-Met-puromycin
show the reaction diagram
-
-
-
-
ir
formylmethionyl-tRNA + alpha-hydroxy-puromycin
tRNA + formylmethionyl-alpha-hydroxy-puromycin
show the reaction diagram
-
ester linkage
-
?
formylmethionyl-tRNA + puromycin
tRNA + formylmethionyl-puromycin
show the reaction diagram
GlcNAc-MurNGlyc-L-Ala1-D-iGln2-meso-DapNH23-D-Ala4 + D-methionine
GlcNAc-MurNGlyc-L-Ala1-D-iGln2-meso-DapNH23-D-Met4 + D-alanine
show the reaction diagram
-
-
-
-
?
L-Phe-tRNA + puromycin
tRNA + L-Phe-puromycin
show the reaction diagram
-
-
-
-
?
Met-tRNA + cytidine-cytidine-hydroxypuromycin
tRNA + Met-cytidine-cytidine-hydroxypuromycin
show the reaction diagram
-
-
-
-
?
Met-tRNA + cytidine-cytidineadenosine-phenylalanine-caproic acid
?
show the reaction diagram
-
-
-
-
?
Met-tRNA + cytidine-hydroxypuromycin
tRNA + Met-cytidine-hydroxypuromycin
show the reaction diagram
-
-
-
-
?
Met-tRNA + cytidine-puromycin
tRNA + Met-cytidine-puromycin
show the reaction diagram
-
-
-
-
?
Met-tRNA + puromycin
tRNA + Met-puromycin
show the reaction diagram
-
-
-
-
?
N-AcMet-tRNA + puromycin
tRNA + N-AcMet-puromycin
show the reaction diagram
-
-
-
?
N-AcPhe-tRNA + puromycin
tRNA + N-AcPhe-puromycin
show the reaction diagram
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
show the reaction diagram
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
show the reaction diagram
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl-aminoacyl-tRNA2
show the reaction diagram
phenylalanyl-tRNA + puromycin
tRNA + phenylalanyl-puromycin
show the reaction diagram
polylysyl-tRNA + puromycin
tRNA + polylysyl-puromycin
show the reaction diagram
polyphenylalanyl-tRNA + puromycin
tRNA + polyphenylalanyl-puromycin
show the reaction diagram
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
peptidyl-tRNA1 + alpha-aminoacyl-tRNA2
tRNA1 + peptidyl-amino-tRNA2
show the reaction diagram
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zn2+
-
contains zinc
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
40S subunits of ribosomes
-
inhibition proportional to the 40S-subunit-concentration
-
Amicetin
ampicillin
-
strain 18sH Con-, 60 microg/ml, 50 percent inhibition; strain 18s SAI-, 3 microg/ml, 50 percent inhibition
anisomycin
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
blasticidin S
carbenicillin
-
strain 18sH Con-, 50 microg/ml, 50 percent inhibition; strain 18s SAI-, 0.2 microg/ml, 50 percent inhibition
carbomycin
Cephaloridine
-
strain 18sH Con-, 200 microg/ml, 50 percent inhibition; strain 18s SAI-, 0.1 microg/ml, 50 percent inhibition
cethromycin
-
-
Chloramphenicol
chlortetracycline
-
59% inhibition
clindamycin
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
ertapenem
erythromycin
-
-
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
Gougerotin
-
-
Griseoviridin
-
-
Imipenem
L-arginine
-
-
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
Lincomycin
-
-
linezolid
m-nitrophenylboric acid
-
more potent inhibitor than phenylboric acid
modithromycin
-
-
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
phenylboric acid
-
-
pristinamycin I1
-
-
pristinamycin IIa
-
-
radezolid
-
-
retapamulin
-
-
sparsomycin
spermine
streptogramin A
telithromycin
-
-
Tevenel
-
-
Thiamphenicol
-
-
tiamulin
torezolid phosphate
-
-
valnemulin
additional information
-
the peptidyl transferase center is not inhibited by D-arginine
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
methanol
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
poly-U
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with acetylphenylalanyl-tRNA as donor only
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000058
acetylphenylalanyl-tRNA
-
-
3.2
cytidine-puromycin
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at 37C and pH 7.5
1.1
puromycin
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at 37C and pH 7.5
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0102 - 0.333
AcPhe-tRNA
-
19
cytidine-puromycin
Escherichia coli
-
at 37C and pH 7.5
0.138
formylmethionyl-tRNA
Escherichia coli
-
when NH4Cl ribosomal wash is present
0.17
puromycin
Escherichia coli
-
at 37C and pH 7.5
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00067
anisomycin
-
-
0.0002
blasticidin S
-
-
0.00007 - 0.007
Chloramphenicol
0.0058
Gly-chloramphenicol
-
-
0.09
Gly-Phe-chloramphenicol
-
-
0.02
L-Phe-chloramphenicol
-
-
0.002
L-Phe-Gly-chloramphenicol
-
-
0.46
m-nitrophenylboric acid
-
-
33
N1,N12-Diacetylspermine
-
-
12.9
N1,N12-dipivaloylspermine
-
-
5
N1-acetylspermine
-
-
0.52
phenylboric acid
-
-
0.00013 - 0.00022
sparsomycin
3.2
spermine
-
-
0.00017
Tevenel
-
-
0.000045
Thiamphenicol
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.1 - 7.4
-
-
7.5 - 8.25
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2 - 9.5
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0
-
enzyme assay
20
-
enzyme assay
35
-
enzyme assay
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
salt-washed ribosomes
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Streptococcus suis (strain 05ZYH33)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
27600
-
x * 27600, LtdA, calculated from amino acid sequence
28500
-
x * 28500, LtdA, calculated from amino acid sequence
29800
-
x * 29800, LtdD, calculated from amino acid sequence
38100
-
x * 38100, LtdE, calculated from amino acid sequence
40200
-
x * 40200, LtdE, calculated from amino acid sequence
44000
-
x * 44000, LtdB, calculated from amino acid sequence
44900
-
x * 44900, LtdB, calculated from amino acid sequence
46200
-
x * 46200, LtdF, calculated from amino acid sequence
49600
-
x * 49600, LtdC, calculated from amino acid sequence
49700
-
x * 49700, LtdC, calculated from amino acid sequence; x * 49700, LtdG, calculated from amino acid sequence
67000
-
x * 67000, calculated from amino acid sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
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
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-70C, both ribosomes and factors washable from ribosomes
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
metal affinity column chromatography and gel filtration
-
Ni-NTA agarose chromatography
-
Ni-NTA column chromatography
Ni-NTA column chromatography and Superdex 75 gel filtration
-
Ni-NTA resin column chromatography and Superdex 200 gel filtration
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli DH5alpha cells
-
expressed in Thermus aquaticus
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the enzyme is upregulated in response to Cpx envelope stress response-inducing conditions
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K372A
-
the mutant shows 7% of wild type activity
K372A/R437A
-
the mutant shows 2% of wild type activity
R437A
-
the mutant shows 26% of wild type activity
W425A
-
the mutant shows 0.04% of wild type activity
A2451U
-
with puromycin as an acceptor substrate, the catalytic rate of the mutant enzyme decreases about 150fold relative to wild type enzyme
C74G
-
1.9fold inhibition in the rate of translocation of tRNA
G2252C
-
the rate of peptidyl transferase reaction is 100fold decreased
A2451U
-
the base identity at this highly conserved residue is not absolutely critical for peptide bond synthesis
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine