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Literature summary extracted from

  • Lehmann, J.
    Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids (2017), RNA, 23, 229-239 .
    View publication on PubMedView publication on EuropePMC

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.3.2.12 additional information
-
 additional information Michaelis-Menten kinetics Escherichia coli

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.3.2.12 ribosome
-
 Escherichia coli 5840
-

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.3.2.12 Lys-tRNALys + Phe-tRNAPhe Escherichia coli
-
 tRNALys + Lys(Phe-tRNA2)
-
 ?
2.3.2.12 Met-Phe-tRNAPhe + Phe-tRNAPhe Escherichia coli
-
 tRNAPhe + Met-Phe(Phe-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2 Escherichia coli
-
 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.3.2.12 Escherichia coli
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.3.2.12 Lys-tRNALys + Phe-tRNAPhe
-
 Escherichia coli tRNALys + Lys(Phe-tRNA2)
-
 ?
2.3.2.12 Lys-tRNALys + puromycin
-
 Escherichia coli tRNALys + Lys-puromycin
-
 ?
2.3.2.12 Met-Phe-tRNAPhe + Phe-tRNAPhe
-
 Escherichia coli tRNAPhe + Met-Phe(Phe-tRNA2)
-
 ?
2.3.2.12 additional information the nature of the side-chain of A-aa acceptor substrates strongly affects the acceptor activity in the peptidyl transfer reaction on the ribosome. This activity is furthermore affected by the nature of the P-site donor. The most efficient (A-Phe) and the least active (A-Gly, A-DPhe) acceptors are, the same in all three donor configurations so far systematically tested. With Lys(n)-tRNA on the P-site, A-Phe has a catalytic rate constant (kcat) about 50-100fold higher than A-Gly. A-Phe has approximately the same acceptor activity as Pm, for which kcat has independently been established to about 5/sec with Met-Phe-tRNAPhe as the donor substrate, under standard conditions. The D-enantiomers of amino acids with only one carbon atom in the side-chain (Ala, Ser, and Cys) are all incorporated almost as efficiently as their L-enantiomer counterparts. With alanyl-tRNA as the A-site substrate, the Calpha pinching mechanism can orient both L- and D-enantiomers for nucleophilic attack. Substrate specificity, detailed overview. Puromycin (Pm) and analogues still react in the uninduced state plausibly because ribosome residue U2585 forms a hydrogen bond with Pm(2'-OH), thus opening the gate for nucleophilic attack without full induction Escherichia coli ?
-
-
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2
-
 Escherichia coli tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.3.2.12 peptidyl transferase center
-
 Escherichia coli
2.3.2.12 PTC
-
 Escherichia coli

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.3.2.12 25 37 assay at Escherichia coli

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.3.2.12 7.5
-
 assay at Escherichia coli

General Information

EC Number General Information Comment Organism
2.3.2.12 additional information the ribosome is capable of polymerizing at a similar rate at least 20 different kinds of amino acids from aminoacyl-tRNA carriers while using just one catalytic site, the peptidyl-transferase center (PTC). The PTC uses an induced-fit mechanism, analysis of published ribosome structures supports the hypothesis that the induced fit eliminates unreactive rotamers predominantly populated for some A-site aminoacyl esters before induction. The hypothesis is fully consistent with the wealth of kinetic data obtained with these substrates. Induction constrains the amino acids into a reactive conformation in a side-chain independent manner. The rationale of the PTC structural organization confers to the ribosome the very unusual ability to handle large as well as small substrates. An induced fit (or conformational change) is identified in the peptidyl-transferase center (PTC) of the ribosome, in which the binding of the 3' acceptor arm of an A-site aminoacyl tRNA triggers a major rearrangement of two ribosome residues, U2506 and U2585, modeling, overview. The room available inside the PTC cavity and its flexibility in the uninduced state leave some conformational freedom to the esterified amino acids. The induced fit orients the aminoacyl ester for nucleophilic attack. PTC structure-function relationship, detailed overview Escherichia coli