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Literature summary for 3.6.5.3 extracted from

  • Warias, M.; Grubmueller, H.; Bock, L.V.
    tRNA dissociation from EF-Tu after GTP hydrolysis primary steps and antibiotic inhibition (2019), Biophys. J., 117, 1-11 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.6.5.3

Inhibitors

Inhibitors Comment Organism Structure
kirromycin KIR, an antibiotic that directly binds to the interface of EF-Tu domains D1 and D3 and prevents dissociation of EF-Tu from the ribosome and from the amino acid-tRNA after GTP hydrolysis. Kirromycin binds within the D1-D3 interface, sterically blocking its closure, but does not prevent hydrolysis. With KIR bound, the overall conformation of EF-Tu remains close to the GTP-bound conformation after hydrolysis, both on and off the ribosome Escherichia coli
kirromycin KIR, an antibiotic that directly binds to the interface of EF-Tu domains D1 and D3 and prevents dissociation of EF-Tu from the ribosome and from the amino acid-tRNA after GTP hydrolysis. Kirromycin binds within the D1-D3 interface, sterically blocking its closure, but does not prevent hydrolysis. With KIR bound, the overall conformation of EF-Tu remains close to the GTP-bound conformation after hydrolysis, both on and off the ribosome Thermus aquaticus

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Thermus aquaticus
Mg2+ required Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
GTP + H2O Thermus aquaticus
-
 GDP + phosphate
-
 ?
GTP + H2O Escherichia coli
-
 GDP + phosphate
-
 ?

Organism

Organism UniProt Comment Textmining
Escherichia coli P0CE47
-
-
Thermus aquaticus Q01698
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
GTP + H2O
-
 Thermus aquaticus GDP + phosphate
-
 ?
GTP + H2O
-
 Escherichia coli GDP + phosphate
-
 ?
GTP + H2O after GTP hydrolysis and phosphate release, the loss of interactions between the nucleotide and the switch 1 loop of EF-Tu allows domain D1 of EF-Tu to rotate relative to domains D2 and D3 and leads to an increased flexibility of the switch 1 loop. This rotation induces a closing of the D1-D3 interface and an opening of the D1-D2 interface. The opening of the D1-D2 interface, which binds the CCA tail of the tRNA, weakens the crucial EF-Tu-tRNA interactions, which lowers tRNA binding affinity, representing the first step of tRNA release Thermus aquaticus GDP + phosphate
-
 ?
GTP + H2O after GTP hydrolysis and phosphate release, the loss of interactions between the nucleotide and the switch 1 loop of EF-Tu allows domain D1 of EF-Tu to rotate relative to domains D2 and D3 and leads to an increased flexibility of the switch 1 loop. This rotation induces a closing of the D1-D3 interface and an opening of the D1-D2 interface. The opening of the D1-D2 interface, which binds the CCA tail of the tRNA, weakens the crucial EF-Tu-tRNA interactions, which lowers tRNA binding affinity, representing the first step of tRNA release Escherichia coli GDP + phosphate
-
 ?
additional information upon GTP hydrolysis, phosphate release results in a loss of the switch 1 loop anchoring to the rest of D1, which frees D1 to rotate around the switch 2 helix. This rotation closes the D1-D3 interface and opens the D2-D3 interface, possibly decreasing the interaction of EF-Tu with the amino acid and the CCA tail of the tRNA and, therefore, the affinity of the tRNA to EF-Tu Thermus aquaticus ?
-
-
additional information upon GTP hydrolysis, phosphate release results in a loss of the switch 1 loop anchoring to the rest of D1, which frees D1 to rotate around the switch 2 helix. This rotation closes the D1-D3 interface and opens the D2-D3 interface, possibly decreasing the interaction of EF-Tu with the amino acid and the CCA tail of the tRNA and, therefore, the affinity of the tRNA to EF-Tu Escherichia coli ?
-
-

Synonyms

Synonyms Comment Organism
EF-Tu
-
 Thermus aquaticus
EF-Tu
-
 Escherichia coli

General Information

General Information Comment Organism
additional information EF-Tu in the GTPase-activated conformation, three-dimensional structure. The gamma-phosphate of GTP interacts with EF-Tu via the P-loop (V20, D21), the switch 1 loop (T61), and the switch 2 loop (G83). The switch 1 loop in turn is involved in the binding of EF-Tu to the tRNA (nucleotides 1-3 and 73-75). The conformational changes of the ribosome-EF-Tu complex and the effect of GTP hydrolysis as well as of KIR are modeled by all-atom explicit-solvent molecular dynamics simulations with GTP and with GDP and KIR as well as with GDP in the absence of KIR Thermus aquaticus
additional information EF-Tu in the GTPase-activated conformation, three-dimensional structure. The gamma-phosphate of GTP interacts with EF-Tu via the P-loop (V20, D21), the switch 1 loop (T61), and the switch 2 loop (G83). The switch 1 loop in turn is involved in the binding of EF-Tu to the tRNA (nucleotides 1-3 and 73-75). The conformational changes of the ribosome-EF-Tu complex and the effect of GTP hydrolysis as well as of KIR are modeled by all-atom explicit-solvent molecular dynamics simulations with GTP and with GDP and KIR as well as with GDP in the absence of KIR Escherichia coli
physiological function elongation factor Tu (EF-Tu) is a central part of the bacterial translation machinery. During each round of translation elongation, EF-Tu delivers an aminoacyl-tRNA (aatRNA) to the ribosome in a ternary complex with GTP. The successful decoding of the messenger RNA codon by the aa-tRNA leads to a closing of the small ribosomal subunit (30S), which in turn docks EF-Tu at the sarcin-ricin loop of the large subunit (50S) in the GTPase-activated (GA) state. The transition of EF-Tu into a reorganized catalytic configuration in the GTPase-activated state catalyzes GTP hydrolysis to GDP, followed by the release of inorganic phosphate (Pi) and a conformational change of EF-Tu Thermus aquaticus
physiological function elongation factor Tu (EF-Tu) is a central part of the bacterial translation machinery. During each round of translation elongation, EF-Tu delivers an aminoacyl-tRNA (aatRNA) to the ribosome in a ternary complex with GTP. The successful decoding of the messenger RNA codon by the aa-tRNA leads to a closing of the small ribosomal subunit (30S), which in turn docks EF-Tu at the sarcin-ricin loop of the large subunit (50S) in the GTPase-activated (GA) state. The transition of EF-Tu into a reorganized catalytic configuration in the GTPase-activated state catalyzes GTP hydrolysis to GDP, followed by the release of inorganic phosphate (Pi) and a conformational change of EF-Tu Escherichia coli