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Information on EC 2.3.2.12 - peptidyltransferase and Organism(s) Mycobacterium tuberculosis and UniProt Accession O53223

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EC Tree
     2 Transferases
         2.3 Acyltransferases
             2.3.2 Aminoacyltransferases
                2.3.2.12 peptidyltransferase
IUBMB 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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This record set is specific for:
Mycobacterium tuberculosis
UNIPROT: O53223
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The taxonomic range for the selected organisms is: Mycobacterium tuberculosis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
peptidyl transferase, peptidyl transferase center, peptidyltransferase, ribosomal peptidyl transferase, ldtmt2, ribosomal peptidyltransferase, ribosomal protein l27, ptase, peptidoglycan transpeptidase, peptidyltransferase centre, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
L,D-transpeptidase 2
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L,D-transpeptidase
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L,D-transpeptidase 2
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peptidyl transferase center
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ribosomal peptidyltransferase
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-
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transpeptidase
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
aminoacyl group transfer
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-
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peptidyl group transfer
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-
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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.
CAS REGISTRY NUMBER
COMMENTARY hide
9059-29-4
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
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
-
-
-
-
?
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
show the reaction diagram
peptidyl-tRNA1 + aminoacyl-tRNA2
tRNA1 + peptidyl(aminoacyl-tRNA2)
show the reaction diagram
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine
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i.e. ZINC19595411
1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine
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i.e. ZINC22812775
doripenem
eperezolid
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ZINC03813328
ertapenem
Imipenem
linezolid
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ZINC02008866
meropenem
posizolid
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ZINC03982517
radezolid
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ZINC40379938
sutezolid
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ZINC03810825
tedizolid
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ZINC43100953
additional information
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improved small molecule inhibitors of the Mtb ribosomal PTC are obtained using a combination of NMR transverse relaxation times (T2) and computational chemistry approaches, inhibitor design from scaffolds, docking study, overview. Two phenylthiazole derivatives with low IC50 values are predicted by machine learning models as effective inhibitors. Screening of the ZINC database. Predicted binding of oxazolidinone antibiotics that target the ribosomal PTC
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
the enzyme catalyzes the formation of 3 -> 3 peptidoglycan cross-links of the cell wall and facilitates resistance against classical beta-lactams
evolution
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for the ribosomal PTC used (U2673-C2836), there is 100% identity between Mycobacterium tuberculosis and Mycobacterium smegmatis. The Staphylococcus aureus peptidyl transferase center (PTC) is homologous to Mycobacterium tuberculosis PTC
malfunction
physiological function
additional information
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the enzyme is part of the peptidyl transferase center (PTC)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
27600
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x * 27600, LtdA, calculated from amino acid sequence
29800
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x * 29800, LtdD, calculated from amino acid sequence
40200
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x * 40200, LtdE, calculated from amino acid sequence
44900
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x * 44900, LtdB, calculated from amino acid sequence
49600
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x * 49600, LtdC, calculated from amino acid sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA resin column chromatography and Superdex 200 gel filtration
Ni-NTA column chromatography
Ni-NTA column chromatography and Superdex 75 gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli BL21(DE3) cells
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Tam, B.; Sherf, D.; Cohen, S.; Eisdorfer, S.A.; Perez, M.; Soffer, A.; Vilenchik, D.; Akabayov, S.R.; Wagner, G.; Akabayov, B.
Discovery of small-molecule inhibitors targeting the ribosomal peptidyl transferase center (PTC) of M. tuberculosis
Chem. Sci.
10
8764-8767
2019
Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 27294, Mycobacterium tuberculosis H37Rv, Mycolicibacterium smegmatis, Mycolicibacterium smegmatis ATCC 700084, Mycolicibacterium smegmatis mc(2)155, Staphylococcus aureus
Manually annotated by BRENDA team