EC Number | Crystallization (Comment) | Organism |
---|---|---|
2.3.2.12 | Thermus thermophilus 70S ribosomes complexed with mRNA and P-site (fMet-tRNAifMet) and A-site (Phe-tRNAPhe) substrates, co-crystallization of inhibitor madumycin II, sitting drop vapor diffusion method, 70S ribosome complexes are formed in buffer containing 5 mM HEPES-KOH, pH 7.6, 50 mM KCl, 10 mM NH4Cl, and 10 mM Mg(CH3COO)2, and then crystallized in buffer containing 100 mM Tris-HCl, pH 7.6, 2.9% w/v PEG 20000, 7-12% v/v MPD, 100-200 mM arginine, 0.5 mM 2-mercaptoethanol, 19°C, X-ray diffraction structure determination and analysis at 2.8 A resolution, molecular replacement, structure modeling | Thermus thermophilus |
EC Number | Inhibitors | Comment | Organism | Structure |
---|---|---|---|---|
2.3.2.12 | madumycin II | i.e. MADU, an alanine-containing streptogramin A antibiotic, inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. It allows binding of the tRNAs to the ribosomal A and P sites, but prevents correct positioning of their CCA-ends into the PTC thus making peptide bond formation impossible. Drug-induced rearrangement of nucleotides U2506 and U2585 of the 23S rRNA resulting in the formation of the U2506-G2583 wobble pair that is attributed to a catalytically inactive state of the PTC. At 0.005 mM concentration, MADU reduces the efficiency of protein synthesis by over 100fold | Escherichia coli | |
2.3.2.12 | madumycin II | i.e. MADU, an alanine-containing streptogramin A antibiotic, inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. It allows binding of the tRNAs to the ribosomal A and P sites, but prevents correct positioning of their CCA-ends into the PTC thus making peptide bond formation impossible. Drug-induced rearrangement of nucleotides U2506 and U2585 of the 23S rRNA resulting in the formation of the U2506-G2583 wobble pair that is attributed to a catalytically inactive state of the PTC. Structures of inhibitor madumycin II in complex with the 70S ribosome and A- and P-tRNAs, overview | Thermus thermophilus | |
2.3.2.12 | additional information | streptogramins A is a class of protein synthesis inhibitors that target the peptidyl transferase center (PTC) on the large subunit of the ribosome | Escherichia coli | |
2.3.2.12 | additional information | streptogramins A is a class of protein synthesis inhibitors that target the peptidyl transferase center (PTC) on the large subunit of the ribosome. In ribosome complex with mRNA and tRNAs, the binding site of madumycin II is very similar to the binding sites of virginiamycin M, dalfopristin, or flopristin (all proline-containing type A streptogramin antibiotics) | Thermus thermophilus |
EC Number | Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|---|
2.3.2.12 | ribosome | 70S ribosome | Thermus thermophilus | 5840 | - |
2.3.2.12 | ribosome | 70S ribosome | Escherichia coli | 5840 | - |
EC Number | Metals/Ions | Comment | Organism | Structure |
---|---|---|---|---|
2.3.2.12 | Mg2+ | required | Thermus thermophilus | |
2.3.2.12 | Mg2+ | required | Escherichia coli |
EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|---|
2.3.2.12 | peptidyl-tRNA1 + aminoacyl-tRNA2 | Thermus thermophilus | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
2.3.2.12 | peptidyl-tRNA1 + aminoacyl-tRNA2 | Escherichia coli | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? |
EC Number | Organism | UniProt | Comment | Textmining |
---|---|---|---|---|
2.3.2.12 | Escherichia coli | - |
- |
- |
2.3.2.12 | Thermus thermophilus | - |
- |
- |
EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|---|
2.3.2.12 | fMet-Phe-tRNAPhe + puromycin | - |
Thermus thermophilus | tRNAPhe + fMet-Phe-puromycin | - |
? | |
2.3.2.12 | fMet-Phe-tRNAPhe + puromycin | - |
Escherichia coli | tRNAPhe + fMet-Phe-puromycin | - |
? | |
2.3.2.12 | fMet-tRNAfMet + Phe-tRNAPhe | - |
Thermus thermophilus | tRNAfMet + fMet(Phe-tRNA2) | - |
? | |
2.3.2.12 | fMet-tRNAfMet + Phe-tRNAPhe | - |
Escherichia coli | tRNAfMet + fMet(Phe-tRNA2) | - |
? | |
2.3.2.12 | fMet-Val-tRNAVal + Phe-tRNAPhe | - |
Thermus thermophilus | tRNAVal + fMet-Val(Phe-tRNA2) | - |
? | |
2.3.2.12 | fMet-Val-tRNAVal + Phe-tRNAPhe | - |
Escherichia coli | tRNAVal + fMet-Val(Phe-tRNA2) | - |
? | |
2.3.2.12 | additional information | the peptidyl transferase reaction is monitored by fMet-Phe dipeptide, fMet-Phe-puromycin, and fMet-Val-Phe tripeptide formation assays | Thermus thermophilus | ? | - |
- |
|
2.3.2.12 | additional information | the peptidyl transferase reaction is monitored by fMet-Phe dipeptide, fMet-Phe-puromycin, and fMet-Val-Phe tripeptide formation assays | Escherichia coli | ? | - |
- |
|
2.3.2.12 | peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Thermus thermophilus | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
2.3.2.12 | peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Escherichia coli | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? |
EC Number | Synonyms | Comment | Organism |
---|---|---|---|
2.3.2.12 | peptidyl transferase center | - |
Thermus thermophilus |
2.3.2.12 | peptidyl transferase center | - |
Escherichia coli |
2.3.2.12 | PTC | - |
Thermus thermophilus |
2.3.2.12 | PTC | - |
Escherichia coli |
EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|---|
2.3.2.12 | 37 | - |
assay at | Thermus thermophilus |
2.3.2.12 | 37 | - |
assay at | Escherichia coli |
EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|---|
2.3.2.12 | 7.5 | - |
assay at | Thermus thermophilus |
2.3.2.12 | 7.5 | - |
assay at | Escherichia coli |
EC Number | IC50 Value | IC50 Value Maximum | Comment | Organism | Inhibitor | Structure |
---|---|---|---|---|---|---|
2.3.2.12 | 0.0003 | - |
pH 7.5, 37°C | Escherichia coli | madumycin II |
EC Number | General Information | Comment | Organism |
---|---|---|---|
2.3.2.12 | additional information | the enzyme is part of the peptidyl transferase center (PTC) | Thermus thermophilus |
2.3.2.12 | additional information | the enzyme is part of the peptidyl transferase center (PTC) | Escherichia coli |