BRENDA - Enzyme Database

Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids

Lehmann, J.; RNA 23, 229-239 (2017)

Data extracted from this reference:

KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
2.3.2.12
additional information
-
additional information
Michaelis-Menten kinetics
Escherichia coli
Localization
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
2.3.2.12
ribosome
-
Escherichia coli
5840
-
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
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
Commentary
Textmining
2.3.2.12
Escherichia coli
-
-
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
2.3.2.12
Lys-tRNALys + Phe-tRNAPhe
-
760119
Escherichia coli
tRNALys + Lys(Phe-tRNA2)
-
-
-
?
2.3.2.12
Lys-tRNALys + puromycin
-
760119
Escherichia coli
tRNALys + Lys-puromycin
-
-
-
?
2.3.2.12
Met-Phe-tRNAPhe + Phe-tRNAPhe
-
760119
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
760119
Escherichia coli
?
-
-
-
-
2.3.2.12
peptidyl-tRNA1 + aminoacyl-tRNA2
-
760119
Escherichia coli
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
?
Synonyms
EC Number
Synonyms
Commentary
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]
Commentary
Organism
2.3.2.12
25
37
assay at
Escherichia coli
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
2.3.2.12
7.5
-
assay at
Escherichia coli
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
2.3.2.12
additional information
-
additional information
Michaelis-Menten kinetics
Escherichia coli
Localization (protein specific)
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
2.3.2.12
ribosome
-
Escherichia coli
5840
-
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
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)
-
-
?
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
2.3.2.12
Lys-tRNALys + Phe-tRNAPhe
-
760119
Escherichia coli
tRNALys + Lys(Phe-tRNA2)
-
-
-
?
2.3.2.12
Lys-tRNALys + puromycin
-
760119
Escherichia coli
tRNALys + Lys-puromycin
-
-
-
?
2.3.2.12
Met-Phe-tRNAPhe + Phe-tRNAPhe
-
760119
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
760119
Escherichia coli
?
-
-
-
-
2.3.2.12
peptidyl-tRNA1 + aminoacyl-tRNA2
-
760119
Escherichia coli
tRNA1 + peptidyl(aminoacyl-tRNA2)
-
-
-
?
Temperature Optimum [C] (protein specific)
EC Number
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
2.3.2.12
25
37
assay at
Escherichia coli
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
2.3.2.12
7.5
-
assay at
Escherichia coli
General Information
EC Number
General Information
Commentary
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
General Information (protein specific)
EC Number
General Information
Commentary
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