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7-cyano-7-carbaguanine in tRNA + NH3 = 7-carboximidamide-guanine in tRNA
7-cyano-7-carbaguanine in tRNA + NH3 = 7-carboximidamide-guanine in tRNA
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7-cyano-7-carbaguanine in tRNA + NH3 = 7-carboximidamide-guanine in tRNA
Asp28 deprotonates Cys21, enabling it to nucleophilically attack the nitrile carbon of preQ0 to produce the covalent thioimide intermediate. The ammonium cation, binding in the pocket defined by Asp28 and the pi-system of Tyr90, is deprotonated by Asp28, allowing the neutral ammonia to attack the thioimide carbon from the Tyr90 side (the face of preQ0 facing the protein core). Proton transfers appear to be facilitated in this process via a tightly bound water molecule observed in the preQ0-bound structure that is H-bonded to His62 and the thioimide nitrogen atom. Collapse of the resulting diaminothioorthoester intermediate via cleavage of the carbon-sulfur bond then provides archaeosine-modified tRNA
7-cyano-7-carbaguanine in tRNA + NH3 = 7-carboximidamide-guanine in tRNA
Asp28 deprotonates Cys21, enabling it to nucleophilically attack the nitrile carbon of preQ0 to produce the covalent thioimide intermediate. The ammonium cation, binding in the pocket defined by Asp28 and the pi-system of Tyr90, is deprotonated by Asp28, allowing the neutral ammonia to attack the thioimide carbon from the Tyr90 side (the face of preQ0 facing the protein core). Proton transfers appear to be facilitated in this process via a tightly bound water molecule observed in the preQ0-bound structure that is H-bonded to His62 and the thioimide nitrogen atom. Collapse of the resulting diaminothioorthoester intermediate via cleavage of the carbon-sulfur bond then provides archaeosine-modified tRNA
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7-cyano-7-carbaguanine in tRNA + NH3 = 7-carboximidamide-guanine in tRNA
Asp28 deprotonates Cys21, enabling it to nucleophilically attack the nitrile carbon of preQ0 to produce the covalent thioimide intermediate. The ammonium cation, binding in the pocket defined by Asp28 and the pi-system of Tyr90, is deprotonated by Asp28, allowing the neutral ammonia to attack the thioimide carbon from the Tyr90 side (the face of preQ0 facing the protein core). Proton transfers appear to be facilitated in this process via a tightly bound water molecule observed in the preQ0-bound structure that is H-bonded to His62 and the thioimide nitrogen atom. Collapse of the resulting diaminothioorthoester intermediate via cleavage of the carbon-sulfur bond then provides archaeosine-modified tRNA
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7-cyano-7-carbaguanine in tRNA + NH3
7-carboximidamide-guanine in tRNA
7-cyano-7-carbaguanosine15 in tRNA + NH4+
archaeosine15 in tRNA
additional information
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7-cyano-7-carbaguanine in tRNA + NH3
7-carboximidamide-guanine in tRNA
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7-cyano-7-carbaguanine in tRNA + NH3
7-carboximidamide-guanine in tRNA
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7-cyano-7-carbaguanine in tRNA + NH3
7-carboximidamide-guanine in tRNA
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7-cyano-7-carbaguanosine15 in tRNA + NH4+
archaeosine15 in tRNA
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7-cyano-7-carbaguanosine15 in tRNA + NH4+
archaeosine15 in tRNA
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7-cyano-7-carbaguanosine15 in tRNA + NH4+
archaeosine15 in tRNA
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additional information
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substrate binding structures, overview
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additional information
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QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0 ) base of preQ0-modified tRNA to a formamidino group
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additional information
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the enzyme is QueF-L an amidinotransferase involved in the pathway of G+ modified tRNA. Substrate is preQ0-modified tRNA. The thioimide intermediate is attacked by ammonia. Glutamine is not the ammonia donor, and the enzyme is only able to utilize free NH4+
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additional information
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the enzyme is QueF-L an amidinotransferase involved in the pathway of G+ modified tRNA. Substrate is preQ0-modified tRNA. The thioimide intermediate is attacked by ammonia. Glutamine is not the ammonia donor, and the enzyme is only able to utilize free NH4+
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additional information
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substrate binding structures, overview
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additional information
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QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0 ) base of preQ0-modified tRNA to a formamidino group
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additional information
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substrate binding structures, overview
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additional information
?
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QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0 ) base of preQ0-modified tRNA to a formamidino group
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evolution
despite distinct catalytic functions, phylogenetic distributions, and only 19% sequence identity, the two enzymes, QueF and QueF-L, share a common preQ0 binding pocket, and likely a common mechanism of thioimide formation. Due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. But like QueF, QueF-L possesses an active-site cysteine that serves as a catalytic nucleophile, reacting with the nitrile group to form a covalent thioimide intermediate. The enzymes belong to the tunneling-fold (T-fold) structural superfamily. QueF-L and QueF (from Bacillus subtilis, PDB ID 4F8B, and Vibrio cholerae, PDB ID 3UXJ) exhibit 18-20% sequence identity, structure comparison, detailed overview. The preQ0-binding pocket is defined by a cleft between two subunits from the same pentamer. QueF (EC 1.7.1.13) is unique to bacteria and the Q branch of the pathway and catalyzes the NADPH-dependent reduction of the nitrile group of preQ0 to the amine of preQ1
evolution
the organism lacks an archaeosine synthase, but comprises two proteins that inversely distribute with ArcS and each other. QueF-like (QueF-L), is a homologue of the bacterial enzyme QueF, which catalyzes the NADPH-dependent reduction of preQ0 to 7-aminomethyl-7-deazaguanine (preQ1) in the queuosine pathway
evolution
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despite distinct catalytic functions, phylogenetic distributions, and only 19% sequence identity, the two enzymes, QueF and QueF-L, share a common preQ0 binding pocket, and likely a common mechanism of thioimide formation. Due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. But like QueF, QueF-L possesses an active-site cysteine that serves as a catalytic nucleophile, reacting with the nitrile group to form a covalent thioimide intermediate. The enzymes belong to the tunneling-fold (T-fold) structural superfamily. QueF-L and QueF (from Bacillus subtilis, PDB ID 4F8B, and Vibrio cholerae, PDB ID 3UXJ) exhibit 18-20% sequence identity, structure comparison, detailed overview. The preQ0-binding pocket is defined by a cleft between two subunits from the same pentamer. QueF (EC 1.7.1.13) is unique to bacteria and the Q branch of the pathway and catalyzes the NADPH-dependent reduction of the nitrile group of preQ0 to the amine of preQ1
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evolution
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the organism lacks an archaeosine synthase, but comprises two proteins that inversely distribute with ArcS and each other. QueF-like (QueF-L), is a homologue of the bacterial enzyme QueF, which catalyzes the NADPH-dependent reduction of preQ0 to 7-aminomethyl-7-deazaguanine (preQ1) in the queuosine pathway
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evolution
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despite distinct catalytic functions, phylogenetic distributions, and only 19% sequence identity, the two enzymes, QueF and QueF-L, share a common preQ0 binding pocket, and likely a common mechanism of thioimide formation. Due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. But like QueF, QueF-L possesses an active-site cysteine that serves as a catalytic nucleophile, reacting with the nitrile group to form a covalent thioimide intermediate. The enzymes belong to the tunneling-fold (T-fold) structural superfamily. QueF-L and QueF (from Bacillus subtilis, PDB ID 4F8B, and Vibrio cholerae, PDB ID 3UXJ) exhibit 18-20% sequence identity, structure comparison, detailed overview. The preQ0-binding pocket is defined by a cleft between two subunits from the same pentamer. QueF (EC 1.7.1.13) is unique to bacteria and the Q branch of the pathway and catalyzes the NADPH-dependent reduction of the nitrile group of preQ0 to the amine of preQ1
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evolution
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the organism lacks an archaeosine synthase, but comprises two proteins that inversely distribute with ArcS and each other. QueF-like (QueF-L), is a homologue of the bacterial enzyme QueF, which catalyzes the NADPH-dependent reduction of preQ0 to 7-aminomethyl-7-deazaguanine (preQ1) in the queuosine pathway
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metabolism
in the Euryarchaeota, the last step of the archaeosine biosynthetic pathway involves the amidation of a nitrile group on an archaeosine precursor to give formamidine, a reaction catalyzed by the enzyme archaeosine synthase (ArcS). Most Crenarchaeota lack ArcS, but possess two proteins that inversely distribute with ArcS and each other, and are implicated in G+ biosynthesis. One of these is the protein QueF-like (QueF-L) from Pyrobaculum calidifontis, which demonstrates the catalytic activity of QueF-L. Possible routes to G+-tRNA in Crenarchaeota possessing QueF-like (QueF-L) enzymes compared to the known pathway in Euryarchaeota that utilizes ArcS to carry out the amidation of preQ0-modified tRNA, overview
metabolism
the amidinotransferase QueF-Like (QueF-L), responsible for the final step in the biosynthesis of archaeosine in the D-loop of tRNA in a subset of Crenarchaeota. The archaeal homologue of QueF, QueF-Like (QueF-L), found in a subset of Crenarchaeota that lack ArcS, is capable of producing G+-modified tRNA
metabolism
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the amidinotransferase QueF-Like (QueF-L), responsible for the final step in the biosynthesis of archaeosine in the D-loop of tRNA in a subset of Crenarchaeota. The archaeal homologue of QueF, QueF-Like (QueF-L), found in a subset of Crenarchaeota that lack ArcS, is capable of producing G+-modified tRNA
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metabolism
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in the Euryarchaeota, the last step of the archaeosine biosynthetic pathway involves the amidation of a nitrile group on an archaeosine precursor to give formamidine, a reaction catalyzed by the enzyme archaeosine synthase (ArcS). Most Crenarchaeota lack ArcS, but possess two proteins that inversely distribute with ArcS and each other, and are implicated in G+ biosynthesis. One of these is the protein QueF-like (QueF-L) from Pyrobaculum calidifontis, which demonstrates the catalytic activity of QueF-L. Possible routes to G+-tRNA in Crenarchaeota possessing QueF-like (QueF-L) enzymes compared to the known pathway in Euryarchaeota that utilizes ArcS to carry out the amidation of preQ0-modified tRNA, overview
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metabolism
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the amidinotransferase QueF-Like (QueF-L), responsible for the final step in the biosynthesis of archaeosine in the D-loop of tRNA in a subset of Crenarchaeota. The archaeal homologue of QueF, QueF-Like (QueF-L), found in a subset of Crenarchaeota that lack ArcS, is capable of producing G+-modified tRNA
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metabolism
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in the Euryarchaeota, the last step of the archaeosine biosynthetic pathway involves the amidation of a nitrile group on an archaeosine precursor to give formamidine, a reaction catalyzed by the enzyme archaeosine synthase (ArcS). Most Crenarchaeota lack ArcS, but possess two proteins that inversely distribute with ArcS and each other, and are implicated in G+ biosynthesis. One of these is the protein QueF-like (QueF-L) from Pyrobaculum calidifontis, which demonstrates the catalytic activity of QueF-L. Possible routes to G+-tRNA in Crenarchaeota possessing QueF-like (QueF-L) enzymes compared to the known pathway in Euryarchaeota that utilizes ArcS to carry out the amidation of preQ0-modified tRNA, overview
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physiological function
enzyme QueF-L functions as an amidinotransferase in the biosynthesis of G+-modified tRNA
physiological function
QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0) base of preQ0-modified tRNA to a formamidino group
physiological function
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QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0) base of preQ0-modified tRNA to a formamidino group
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physiological function
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enzyme QueF-L functions as an amidinotransferase in the biosynthesis of G+-modified tRNA
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physiological function
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QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0) base of preQ0-modified tRNA to a formamidino group
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physiological function
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enzyme QueF-L functions as an amidinotransferase in the biosynthesis of G+-modified tRNA
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additional information
in the presence of preQ0, the enzyme reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine similar to the intermediate previously observed in the nitrile reductase QueF. Due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. A large positively charged molecular surface and a docking model suggest simultaneous binding of multiple tRNA molecules and structure-specific recognition of the D-loop by a surface groove. Ligand docking study of wild-type and SeMet-labeled enzyme, overview
additional information
the conservation of Cys21 in QueF-L (Pyrobaculum calidifontis QueF-L numbering) and QueF (Cys55 inBacillus subtilis QueF numbering, PDB ID 4F8B), which in QueF participates in the catalytic mechanism via nucleophilic attack of the thiol group on the nitrile of preQ0 to form a covalent thioimide intermediate, suggests that QueF-L might utilize a similar intermediate in the mechanism to form the formamidine of G+
additional information
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in the presence of preQ0, the enzyme reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine similar to the intermediate previously observed in the nitrile reductase QueF. Due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. A large positively charged molecular surface and a docking model suggest simultaneous binding of multiple tRNA molecules and structure-specific recognition of the D-loop by a surface groove. Ligand docking study of wild-type and SeMet-labeled enzyme, overview
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additional information
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the conservation of Cys21 in QueF-L (Pyrobaculum calidifontis QueF-L numbering) and QueF (Cys55 inBacillus subtilis QueF numbering, PDB ID 4F8B), which in QueF participates in the catalytic mechanism via nucleophilic attack of the thiol group on the nitrile of preQ0 to form a covalent thioimide intermediate, suggests that QueF-L might utilize a similar intermediate in the mechanism to form the formamidine of G+
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additional information
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in the presence of preQ0, the enzyme reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine similar to the intermediate previously observed in the nitrile reductase QueF. Due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. A large positively charged molecular surface and a docking model suggest simultaneous binding of multiple tRNA molecules and structure-specific recognition of the D-loop by a surface groove. Ligand docking study of wild-type and SeMet-labeled enzyme, overview
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additional information
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the conservation of Cys21 in QueF-L (Pyrobaculum calidifontis QueF-L numbering) and QueF (Cys55 inBacillus subtilis QueF numbering, PDB ID 4F8B), which in QueF participates in the catalytic mechanism via nucleophilic attack of the thiol group on the nitrile of preQ0 to form a covalent thioimide intermediate, suggests that QueF-L might utilize a similar intermediate in the mechanism to form the formamidine of G+
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Bon Ramos, A.; Bao, L.; Turner, B.; de Crecy-Lagard, V.; Iwata-Reuyl, D.
QueF-like, a non-homologous archaeosine synthase from the crenarchaeota
Biomolecules
7
E36
2017
Pyrobaculum calidifontis (A3MSP1), Pyrobaculum calidifontis JCM 11548 (A3MSP1)
brenda
Mei, X.; Alvarez, J.; Bon Ramos, A.; Samanta, U.; Iwata-Reuyl, D.; Swairjo, M.A.
Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold
Proteins
85
103-116
2017
Pyrobaculum calidifontis (A3MSP1), Pyrobaculum calidifontis JCM 11548 (A3MSP1), Pyrobaculum calidifontis VA1 (A3MSP1)
brenda
Bon Ramos, A.; Bao, L.; Turner, B.; de Crecy-Lagard, V.; Iwata-Reuyl, D.
QueF-Like, a Non-Homologous Archaeosine Synthase from the Crenarchaeota
Biomolecules
7
36
2017
Pyrobaculum calidifontis (A3MSP1), Pyrobaculum calidifontis JCM 11548 (A3MSP1), Pyrobaculum calidifontis VA1 (A3MSP1)
brenda