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 | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | required | Thermus aquaticus | |
Mg2+ | required | Escherichia coli |
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 | UniProt | Comment | Textmining |
---|---|---|---|
Escherichia coli | P0CE47 | - |
- |
Thermus aquaticus | Q01698 | - |
- |
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 | Comment | Organism |
---|---|---|
EF-Tu | - |
Thermus aquaticus |
EF-Tu | - |
Escherichia coli |
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 |