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evolution
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the dedication of Mg2+ to rate enhancement separates TrmD from O- and N6-methyl transferases. TrmD shows the topologically knotted protein fold
evolution
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the deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life
evolution
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the deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life
evolution
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the enzyme shows strong homology to members of the class I-like methyltransferase superfamily
evolution
archaeal Trm5a, a member of the archaeal Trm5a/b/c family of enzymes involved in the biosynthesis of the wyosine derivatives, division of the family aTrm5 into three subfamilies aTrm5a (further divided into Taw21 and Taw22 which are monofunctional and bifunctional aTrm5a), aTrm5b, and aTrm5c. While the enzymes belonging to these subfamilies do not significantly differ in their AdoMet-binding site, small differences have been observed within the NPPY motif, which, in certain amino-methyltransferases, is involved in the positioning of the target nitrogen atom. In contrast, the N-terminal sequences of the aforementioned enzymes differ substantially, e.g. a small conservative domain called D1 is present in aTrm5b and aTrm5c but absent in most of the aTrm5a proteins. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. Amino acid sequence alignment of Trm5a/b/c family of proteins. Monofunctional and bifunctional aTrm5a enzymes, overview
evolution
archaeal Trm5a, a member of the archaeal Trm5a/b/c family of enzymes involved in the biosynthesis of the wyosine derivatives, division of the family aTrm5 into three subfamilies aTrm5a (further divided into Taw21 and Taw22 which are monofunctional and bifunctional aTrm5a), aTrm5b, and aTrm5c. While the enzymes belonging to these subfamilies do not significantly differ in their AdoMet-binding site, small differences have been observed within the NPPY motif, which, in certain amino-methyltransferases, is involved in the positioning of the target nitrogen atom. In contrast, the N-terminal sequences of the aforementioned enzymes differ substantially, e.g. a small conservative domain called D1 is present in aTrm5b and aTrm5c but absent in most of the aTrm5a proteins. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. Amino acid sequence alignment of Trm5a/b/c/ family of proteins. Monofunctional and bifunctional aTrm5a enzymes, overview
evolution
at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. Trm5 belongs to the class I tRNA methyl transferases. Trm5 is an active monomer that uses the class I-fold. Methanococcus jannaschii MjTrm5 is homologous to human Trm5
evolution
at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. Trm5 belongs to the class I tRNA methyl transferases. Trm5 is an active monomer that uses the class I-fold. MjTrm5 is homologous to human Trm5
evolution
at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. TrmD belongs to the class IV tRNA methyl transferases. TrmD is an obligated dimer that uses the class IV-fold for AdoMet binding. EcTrmD is homologous to Haemophilus influenza TrmD
evolution
at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. TrmD belongs to the class IV tRNA methyl transferases. TrmD is an obligated dimer that uses the class IV-fold for AdoMet binding. Escherichia coli EcTrmD is homologous to Haemophilus influenza TrmD
evolution
during the evolutionary process, some euryarchaeota like Thermococcus and Pyrococcus preserved both the trm5 genes from the crenarchaeal origin as well as the native copy, but others apparently lost the latter. Phylogenetic distribution analyses of trm5 homologues in archaeal genomes allow the identification of three archaeal Trm5 (aTrm5) subfamilies: Trm5a, Trm5b, and Trm5c. Trm5b refers to the native form, while Trm5a refers to the crenarchaeal origin, and Trm5c to other members with divergent Trm5 sequences11. The three Trm5s differ substantially in primary sequences
evolution
in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism
evolution
in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism
evolution
in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism
evolution
phylogenetic analyses revealed that the archaeal Trm5s can be grouped into three categories: Trm5a, Trm5b, and Trm5c, which all perform the N1-methylation of tRNAPhe G37. Trm5a exists in all crenarchaea. On the other hand, Trm5b is ubiquitously found in euryarchaeota, and is regarded as the original Trm5. Trm5c can be originated from euryarchaeota by horizontal gene transfer and exists in two crenarchaeal orders. In addition, both aTrm5b and aTrm5c contain an N-terminal domain named D1, which is responsible for the G19:C56 base pair recognition but may be absent from most aTrm5as. Despite the differences at the N-termini, all Trm5s have the Rossmann fold at the C-termini for catalysis, with the consensus NPPY motif located in the fourth beta-strand. The motif is known to position the nitrogen atom of G37 from the substrate, but specific sequences may vary from this consensus. Structure comparison of Methanococcus jannaschii MjTrm5b and PaTrm5b, overview
evolution
the enzyme TrmD belongs to the 2'-O-methyltransferase family, previously SpoU family of enzymes, conserved motifs in the TrmH (SpoU) and TrmD families, overview. Comparisons of topological knot structures in TrmH (SpoU) and TrmD. AdoMet-dependent enzymes can be divided into more than five classes according to the structure of their catalytic domain. Most methyltransferases have a Rossman fold catalytic domain and are classified as class I enzymes. In contrast, members of SPOUT RNA methyltransferase superfamily are classified as class IV enzymes, whose catalytic domain forms a deep trefoil (topological) knot. TrmD from Aquifex aeolicus belongs to the m1G37 methyltransferases
evolution
the enzyme TrmD belongs to the 2'-O-methyltransferase family, previously SpoU family of enzymes, conserved motifs in the TrmH (SpoU) and TrmD families, overview. Comparisons of topological knot structures in TrmH (SpoU) and TrmD. AdoMet-dependent enzymes can be divided into more than five classes according to the structure of their catalytic domain. Most methyltransferases have a Rossman fold catalytic domain and are classified as class I enzymes. In contrast, members of SPOUT RNA methyltransferase superfamily are classified as class IV enzymes, whose catalytic domain forms a deep trefoil (topological) knot. TrmD from Escherichia coli belongs to the m1G37 methyltransferases
evolution
the enzyme TrmD belongs to the 2'-O-methyltransferase family, previously SpoU family of enzymes, conserved motifs in the TrmH (SpoU) and TrmD families, overview. Comparisons of topological knot structures in TrmH (SpoU) and TrmD. AdoMet-dependent enzymes can be divided into more than five classes according to the structure of their catalytic domain. Most methyltransferases have a Rossman fold catalytic domain and are classified as class I enzymes. In contrast, members of SPOUT RNA methyltransferase superfamily are classified as class IV enzymes, whose catalytic domain forms a deep trefoil (topological) knot. TrmD from Haemophilus influenzae belongs to the m1G37 methyltransferases
evolution
the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases
evolution
the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases.
evolution
the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
evolution
the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. In addition to the methylation of the N1-atom of guanosine, Trm5a catalyzes the methylation of the C7-atom of 4-demethylwyosine, which is the intermediate of the wyosine derivatives found at position 37 of archaeal tRNAPhe. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
evolution
the TrmD knot is closely related to the trefoil-knot in SpoU methyl transferases, which catalyze 2'-O-methylation to RNA ribose for wide-ranging activities. In virtually all aspects of the methyl transfer reaction, TrmD is distinct from related Trm5
evolution
TrmD is broadly conserved in sequence and structure among bacterial species, in both Gram (+) and Gram (-), but it is absent from the eukaryotic and archaeal domains. TrmD is strongly conserved in sequence among evolutionarily diverse bacterial species
evolution
TrmD is broadly conserved in sequence and structure among bacterial species, in both Gram (+) and Gram (-), but it is absent from the eukaryotic and archaeal domains. TrmD is strongly conserved in sequence among evolutionarily diverse bacterial species
evolution
TrmD is broadly conserved in sequence and structure among bacterial species, in both Gram (+) and Gram (-), but it is absent from the eukaryotic and archaeal domains. TrmD is strongly conserved in sequence among evolutionarily diverse bacterial species. In all of the available structures of the TrmD dimer, each monomeric chain is made up of three distinct domains: an N-terminal domain (residues 1-160 in HiTrmD and EcTrmD) for binding AdoMet, a C-terminal domain for binding tRNA (residues 169-246), and a flexible linker in between (residues 161-168)
evolution
TrmD is broadly conserved in sequence and structure among bacterial species, in both Gram (+) and Gram (-), but it is absent from the eukaryotic and archaeal domains. TrmD is strongly conserved in sequence among evolutionarily diverse bacterial species. In all of the available structures of the TrmD dimer, each monomeric chain is made up of three distinct domains: an N-terminal domain (residues 1-160 in HiTrmD and EcTrmD) for binding AdoMet, a C-terminal domain for binding tRNA (residues 169-246), and a flexible linker in between (residues 161-168)
evolution
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tRNA (m1G37) methyltransferase (TrmD), a member of the SpoU-TrmD (SPOUT) RNA methyltransferase family
evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. In addition to the methylation of the N1-atom of guanosine, Trm5a catalyzes the methylation of the C7-atom of 4-demethylwyosine, which is the intermediate of the wyosine derivatives found at position 37 of archaeal tRNAPhe. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
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evolution
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archaeal Trm5a, a member of the archaeal Trm5a/b/c family of enzymes involved in the biosynthesis of the wyosine derivatives, division of the family aTrm5 into three subfamilies aTrm5a (further divided into Taw21 and Taw22 which are monofunctional and bifunctional aTrm5a), aTrm5b, and aTrm5c. While the enzymes belonging to these subfamilies do not significantly differ in their AdoMet-binding site, small differences have been observed within the NPPY motif, which, in certain amino-methyltransferases, is involved in the positioning of the target nitrogen atom. In contrast, the N-terminal sequences of the aforementioned enzymes differ substantially, e.g. a small conservative domain called D1 is present in aTrm5b and aTrm5c but absent in most of the aTrm5a proteins. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. Amino acid sequence alignment of Trm5a/b/c/ family of proteins. Monofunctional and bifunctional aTrm5a enzymes, overview
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evolution
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TrmD is broadly conserved in sequence and structure among bacterial species, in both Gram (+) and Gram (-), but it is absent from the eukaryotic and archaeal domains. TrmD is strongly conserved in sequence among evolutionarily diverse bacterial species
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evolution
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in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. Trm5 belongs to the class I tRNA methyl transferases. Trm5 is an active monomer that uses the class I-fold. MjTrm5 is homologous to human Trm5
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. TrmD belongs to the class IV tRNA methyl transferases. TrmD is an obligated dimer that uses the class IV-fold for AdoMet binding. Escherichia coli EcTrmD is homologous to Haemophilus influenza TrmD
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. Trm5 belongs to the class I tRNA methyl transferases. Trm5 is an active monomer that uses the class I-fold. MjTrm5 is homologous to human Trm5
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evolution
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TrmD is broadly conserved in sequence and structure among bacterial species, in both Gram (+) and Gram (-), but it is absent from the eukaryotic and archaeal domains. TrmD is strongly conserved in sequence among evolutionarily diverse bacterial species
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evolution
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in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. Trm5 belongs to the class I tRNA methyl transferases. Trm5 is an active monomer that uses the class I-fold. MjTrm5 is homologous to human Trm5
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. Trm5 belongs to the class I tRNA methyl transferases. Trm5 is an active monomer that uses the class I-fold. MjTrm5 is homologous to human Trm5
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evolution
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in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism
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evolution
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the deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. TrmD belongs to the class IV tRNA methyl transferases. TrmD is an obligated dimer that uses the class IV-fold for AdoMet binding. Escherichia coli EcTrmD is homologous to Haemophilus influenza TrmD
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. TrmD belongs to the class IV tRNA methyl transferases. TrmD is an obligated dimer that uses the class IV-fold for AdoMet binding. Escherichia coli EcTrmD is homologous to Haemophilus influenza TrmD
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. TrmD belongs to the class IV tRNA methyl transferases. TrmD is an obligated dimer that uses the class IV-fold for AdoMet binding. Escherichia coli EcTrmD is homologous to Haemophilus influenza TrmD
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evolution
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the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a
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evolution
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at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. Trm5 belongs to the class I tRNA methyl transferases. Trm5 is an active monomer that uses the class I-fold. MjTrm5 is homologous to human Trm5
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malfunction
efficiency or accuracy of mitochondrial protein synthesis is decreased in cells lacking m1G37 methylation of mitochondrial tRNAs
malfunction
downregulation of TRM5 by RNAi leads to the expected disappearance of m1G37, but with little effect on cytoplasmic translation. Lack of m1G37 does not globally affect cytosolic translation. On the contrary, lack of TRM5 causes a marked growth phenotype and a significant decrease in mitochondrial functions, including protein synthesis
malfunction
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mutations in TRMT5 are associated with the hypomodification of a guanosine residue at position 37 (G37) of mitochondrial tRNA, this hypomodification is particularly prominent in skeletal muscle. The patients show lactic acidosis and evidence of multiple mitochondrial respiratory-chain-complex deficiencies in skeletal muscle
malfunction
structure-guided mutational analysis of HsTrm5 in comparison to the archaeal enzyme from Methanococcus jannaschii, MjTrm5, overview. Validation of the MjTrm5 ternary structure as a useful model for HsTrm5
malfunction
the ts phenotype of an essential gene mutation S88L in gene trmD can be closely linked to the catalytic defect of the gene product
malfunction
Arabidopsis attrm5a mutants are dwarfed and have short filaments, which leads to reduced seed setting. Proteomics data indicate differences in the abundance of proteins involved in photosynthesis, ribosome biogenesis, oxidative phosphorylation and calcium signalling. Levels of phytohormone auxin and jasmonate are reduced in attrm5a mutant, as well as expression levels of genes involved in flowering, shoot apex cell fate determination, and hormone synthesis and signalling. Taken together, loss-of-function of AtTrm5a impaires m1G and m1I methylation and leads to aberrant protein translation, disturbed hormone homeostasis and developmental defects in Arabidopsis plants
malfunction
deletion of the D1 domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate
malfunction
elimination of TrmD increases protein synthesis frameshifts and causes cell death
malfunction
Lack of m1G37 promotes the tRNA to make +1-frameshifts in a fast mechanism during tRNA translocation from the A- to the P-site on the ribosome, and also in a much slower mechanism during tRNA stalling on the P-site next to an empty A-site
malfunction
mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. Ribosome frameshifting in the absence of TrmD, overview
malfunction
mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. Ribosome frameshifting in the absence of TrmD, overview
malfunction
mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. Ribosome frameshifting in the absence of TrmD, overview
malfunction
mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. Ribosome frameshifting in the absence of TrmD, overview
malfunction
substitutions of individual conservative amino acids of Pyrococcus abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37
malfunction
substitutions of individual conservative amino acids of Pyrococcus abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37
malfunction
the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
malfunction
the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
malfunction
Truncation of the N-terminal D1 domain leads to reduced tRNA binding as well as the methyltransfer activity of PaTrm5b
malfunction
-
the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
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malfunction
-
substitutions of individual conservative amino acids of Pyrococcus abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37
-
malfunction
-
mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. Ribosome frameshifting in the absence of TrmD, overview
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malfunction
-
the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
-
malfunction
-
the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
-
malfunction
-
mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. Ribosome frameshifting in the absence of TrmD, overview
-
malfunction
-
the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
-
malfunction
-
the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
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malfunction
Trametes pubescens 927 / 4 GUTat10.1 / TREU927
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downregulation of TRM5 by RNAi leads to the expected disappearance of m1G37, but with little effect on cytoplasmic translation. Lack of m1G37 does not globally affect cytosolic translation. On the contrary, lack of TRM5 causes a marked growth phenotype and a significant decrease in mitochondrial functions, including protein synthesis
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malfunction
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the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5
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metabolism
a hypertension-associated mitochondrial DNA mutation introduces an m1G37 mutation 4435A->G into human mitochondrial tRNAMet, altering its structure and function, phenotype and pathogenic molecular mechanism, overview. The mutation affects a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. Defective nucleotide modifications of mitochondrial tRNAs are associated with several human diseases. Trm5 is one of the tRNA (m1G37)-methyltransferases that catalyzes the identical tRNA modification, m1G37
metabolism
putative enzymatic pathway leading to the formation of wyosine derivatives in Archaea
metabolism
putative enzymatic pathway leading to the formation of wyosine derivatives in Archaea
metabolism
the enzyme is part of the The biosynthetic pathway of mimG in Pyrococcus abyssi, overview. In archaea, G37 hypermodification in tRNAPhe leads to wyosine derivatives. They are important in reading-frame maintenance during protein synthesis, while the absence of such modifications results in elevated error rates in +1 frame-shifting. Among the modification products, 7-methylwyosine (mimG) is perhaps the earliest and minimalist version of the wyosine derivatives unique to some archaea, and 4-demethylwyosine (imG-14), isowyosine (imG2) have also been identified as intermediates along the pathway. The first biosynthetic step of mimG is the formation of m1G37, catalysed by the S-adenosine-L-methionine (SAM)-dependent tRNA methyltransferase named Trm5, which belongs to class-I methyltransferases. The second step is the complex radical-mediated formation of imG-14, catalyzed by the radical SAM enzyme Taw1. The Trm5 enzyme from the archaeon Pyrococcus abyssi (PaTrm5a) also catalyzes the methylation of C7 on imG-14 to produce imG2 (EC 2.1.1.282), which is further methylated on the N4 position of the imidazo-purine ring by Taw3 to form mimG
metabolism
the wyosine hypermodification found exclusively at G37 of tRNAPhe in eukaryotes and archaea is a very complicated process involving multiple steps and enzymes, and the derivatives are essential for the maintenance of the reading frame during translation. In the archaea Pyrococcus abyssi, two key enzymes from the Trm5 family, named PaTrm5a and PaTrm5b respectively, start the process by forming N1-methylated guanosine (m1G37). In addition, PaTrm5a catalyzes the further methylation of C7 on 4-demethylwyosine (imG-14) to produce isowyosine (imG2) at the same position (cf. EC 2.1.1.282)
metabolism
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putative enzymatic pathway leading to the formation of wyosine derivatives in Archaea
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metabolism
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a hypertension-associated mitochondrial DNA mutation introduces an m1G37 mutation 4435A->G into human mitochondrial tRNAMet, altering its structure and function, phenotype and pathogenic molecular mechanism, overview. The mutation affects a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. Defective nucleotide modifications of mitochondrial tRNAs are associated with several human diseases. Trm5 is one of the tRNA (m1G37)-methyltransferases that catalyzes the identical tRNA modification, m1G37
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metabolism
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a hypertension-associated mitochondrial DNA mutation introduces an m1G37 mutation 4435A->G into human mitochondrial tRNAMet, altering its structure and function, phenotype and pathogenic molecular mechanism, overview. The mutation affects a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. Defective nucleotide modifications of mitochondrial tRNAs are associated with several human diseases. Trm5 is one of the tRNA (m1G37)-methyltransferases that catalyzes the identical tRNA modification, m1G37
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metabolism
-
a hypertension-associated mitochondrial DNA mutation introduces an m1G37 mutation 4435A->G into human mitochondrial tRNAMet, altering its structure and function, phenotype and pathogenic molecular mechanism, overview. The mutation affects a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. Defective nucleotide modifications of mitochondrial tRNAs are associated with several human diseases. Trm5 is one of the tRNA (m1G37)-methyltransferases that catalyzes the identical tRNA modification, m1G37
-
metabolism
-
a hypertension-associated mitochondrial DNA mutation introduces an m1G37 mutation 4435A->G into human mitochondrial tRNAMet, altering its structure and function, phenotype and pathogenic molecular mechanism, overview. The mutation affects a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. Defective nucleotide modifications of mitochondrial tRNAs are associated with several human diseases. Trm5 is one of the tRNA (m1G37)-methyltransferases that catalyzes the identical tRNA modification, m1G37
-
metabolism
-
a hypertension-associated mitochondrial DNA mutation introduces an m1G37 mutation 4435A->G into human mitochondrial tRNAMet, altering its structure and function, phenotype and pathogenic molecular mechanism, overview. The mutation affects a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. Defective nucleotide modifications of mitochondrial tRNAs are associated with several human diseases. Trm5 is one of the tRNA (m1G37)-methyltransferases that catalyzes the identical tRNA modification, m1G37
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physiological function
modification at guanine37 is important for maintaining the reading frame fidelity
physiological function
modified guanosine37 is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation
physiological function
-
the m1G37 modification prevents tRNA frameshifts on the ribosome by assuring correct codon-anticodon pairings, and thus is essential for the fidelity of protein synthesis
physiological function
the m1G37 modification prevents tRNA frameshifts on the ribosome by assuring correct codon-anticodon pairings, and thus is essential for the fidelity of protein synthesis
physiological function
the m1G37 tRNA modification plays an important role in reading frame maintenance in mitochondrial protein synthesis
physiological function
this protein is important for the maintenance of the correct reading frame during translation
physiological function
-
methylation of G37 to form m1G acts to sterically block Watson-Crick base pairing and thereby both maintain an open loop conformation, by blocking base pairing with nucleotides elsewhere in the anticodon loop, and protect against frame shifting by preventing its interaction with the mRNA
physiological function
-
S-adenosyl-L-methionine-dependent methyl transfer in one of the most crucial posttranscriptional modifications to tRNA
physiological function
-
the m1G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome
physiological function
-
the m1G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome
physiological function
TRM5 is responsible for m1G37 formation, m1G37 formation in mitochondria is important for respiration, and TbTRM5 is important for mitochondrial protein synthesis and biogenesis. Mitochondrial TRM5 may be needed to mature unmethylated tRNAs that reach the mitochondria and that can pose a problem for translational fidelity, lack of import specificity between some fully matured and potentially defective tRNA species
physiological function
among various RNA types, tRNA is the most frequently modified type. One such modification in tRNAPhe is the methylation at N1 of G37 (m1G37), which is conserved among all three domains of life. The presence of m1G37 allows effective and rapid aminoacylation of certain archaeal tRNA species by cognate aminoacyl-tRNA synthetases, and prevents misacylation by noncognate aminoacyl-tRNA synthetases, as well as +1 frameshift during translation on the ribosome
physiological function
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bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) catalyzes methyl transfer from S-adenosyl-L-methionine (SAM) to the guanine N1 at nucleotide position 37 in a subset of bacterial tRNA isoacceptors and has proven to be an essential enzyme in most bacterial species
physiological function
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bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) catalyzes methyl transfer from S-adenosyl-L-methionine (SAM) to the guanine N1 at nucleotide position 37 in a subset of bacterial tRNA isoacceptors and has proven to be an essential enzyme in most bacterial species
physiological function
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bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) catalyzes methyl transfer from S-adenosyl-L-methionine (SAM) to the guanine N1 at nucleotide position 37 in a subset of bacterial tRNA isoacceptors and has proven to be an essential enzyme in most bacterial species
physiological function
enzyme TrmD catalyzes the transfer of methyl group from AdoMet to N1-atom of G37 in tRNA to form m1G37
physiological function
enzyme TrmD catalyzes the transfer of methyl group from AdoMet to N1-atom of G37 in tRNA to form m1G37
physiological function
enzyme TrmD catalyzes the transfer of methyl group from AdoMet to N1-atom of G37 in tRNA to form m1G37
physiological function
he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
physiological function
he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
physiological function
he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
physiological function
he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Enzyme Trm5a performs the N1-methylation of tRNA G37, but in addition it also catalyzes the methylation of the C7-atom of 4-demethylwyosine, which is the intermediate of the wyosine derivatives found at position 37 of archaeal tRNAPhe
physiological function
in bacteria, TrmD is a methyl transferase that uses a knotted protein fold to catalyze methyl transfer from S-adenosyl methionine (AdoMet) to G37-tRNA. The product m1G37-tRNA is essential for life as a determinant to maintain protein synthesis reading-frame
physiological function
m1G37 tRNA methyltransferase TrmD catalyzes m1G formation at position 37 in many tRNA isoacceptors and is essential
physiological function
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
physiological function
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
physiological function
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
physiological function
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
physiological function
methylation of guanine at position 37 in RNA is critical for bacterial growth, as this reaction is essential for preventing reading frame shifts during translation and therefore for maintaining the fidelity of protein synthesis. This methylation is catalyzed by the tRNA (guanine37-N1)-methyltransferase (TrmD). TrmD uses S-adenosyl-l-methionine (SAM) as a cofactor and transfers the methyl group to the N1 atom of G37 in tRNA. Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) plays important roles in translation. and is critical for growth of Pseudomonas aeruginosa
physiological function
modified nucleosides on tRNA are critical for decoding processes and protein translation. tRNAs can be modified through 1-methylguanosine (m1G) on position 37, a function mediated by Trm5 homologues. Enzyme AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana. The importance of m1G37 is highlighted by its direct function in the decoding process
physiological function
the methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m1G37 (EC 2.1.1.228) and imG2 (EC 2.1.1.282), two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates
physiological function
the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, Trm5 is required for growth in the single-cell eukaryote Saccharomyces cerevisiae, where it provides the important role of preventing mis-charging of tRNA
physiological function
the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, TrmD is required for growth in several bacterial species, including Escherichia coli and Salmonella
physiological function
the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, TrmD is required for growth in several bacterial species, including Escherichia coli and Salmonella
physiological function
tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe. In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. Methyltransferase aTrm5a/Taw22 likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G (EC 2.1.1.228), and C7-methylation of imG-14 to yield imG2 (EC 2.1.1.282)
physiological function
tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe. In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. Methyltransferase aTrm5a/Taw22 likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G (EC 2.1.1.228), and C7-methylation of imG-14 to yield imG2 (EC 2.1.1.282)
physiological function
-
TrmD catalyzes the transfer of a methyl group from S-adenosyl methionine (SAM) to the N1 position of guanosine 37 in bacterial tRNA when preceded by another guanosine in the sequence. The addition of this marker immediately adjacent to the anticodon acts to improve reading frame maintenance on the ribosome, preventing frameshift errors that would result in truncated and inactive peptides. TrmD is essential for growth in a range of bacterial species from Staphylococcus aureus and Pseudomonas aeruginosa to mycobacteria, including Mycobacterium tuberculosis (Mtb) and Mycobacterium abscessus (Mab)
physiological function
tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential for the maintenance of the reading frame during translation. As a unique member of this enzyme family, Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4-demethylwyosine at position 37 to produce isowyosine
physiological function
while the greatest majority of the tRNA modifying enzymes are nonessential for life, acting for example as a chaperone to modulate tRNA activity, a very small number of these enzymes are absolutely required for cell growth and survival. TrmD is an example of one of these essential enzymes, responsible for methyl transfer from AdoMet to the N1 position of the G37 base to synthesize m1G37 on tRNA. The methylated m1G37 is on the 3?-side of the anticodon, and it is necessary for suppressing tRNA frameshifting during protein synthesis on the ribosome TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism. The Mg2+ dependence is important for regulating Mg2+ transport to Salmonella for survival of the pathogen in the host cell. The trefoil knot of TrmD is required for the catalytic mechanism in three ways. Synthesis of m1G37-tRNA by TrmD is a posttranscriptional event
physiological function
while the greatest majority of the tRNA modifying enzymes are nonessential for life, acting for example as a chaperone to modulate tRNA activity, a very small number of these enzymes are absolutely required for cell growth and survival. TrmD is an example of one of these essential enzymes, responsible for methyl transfer from AdoMet to the N1 position of the G37 base to synthesize m1G37 on tRNA. TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism
physiological function
while the greatest majority of the tRNA modifying enzymes are nonessential for life, acting for example as a chaperone to modulate tRNA activity, a very small number of these enzymes are absolutely required for cell growth and survival. TrmD is an example of one of these essential enzymes, responsible for methyl transfer from AdoMet to the N1 position of the G37 base to synthesize m1G37 on tRNA. TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism. The trefoil knot of TrmD is required for the catalytic mechanism in three ways. Synthesis of m1G37-tRNA by TrmD is a posttranscriptional event
physiological function
while the greatest majority of the tRNA modifying enzymes are nonessential for life, acting for example as a chaperone to modulate tRNA activity, a very small number of these enzymes are absolutely required for cell growth and survival. TrmD is an example of one of these essential enzymes, responsible for methyl transfer from AdoMet to the N1 position of the G37 base to synthesize m1G37 on tRNA. TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism. The trefoil knot of TrmD is required for the catalytic mechanism in three ways. Synthesis of m1G37-tRNA by TrmD is a posttranscriptional event
physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Enzyme Trm5a performs the N1-methylation of tRNA G37, but in addition it also catalyzes the methylation of the C7-atom of 4-demethylwyosine, which is the intermediate of the wyosine derivatives found at position 37 of archaeal tRNAPhe
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physiological function
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tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe. In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. Methyltransferase aTrm5a/Taw22 likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G (EC 2.1.1.228), and C7-methylation of imG-14 to yield imG2 (EC 2.1.1.282)
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physiological function
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while the greatest majority of the tRNA modifying enzymes are nonessential for life, acting for example as a chaperone to modulate tRNA activity, a very small number of these enzymes are absolutely required for cell growth and survival. TrmD is an example of one of these essential enzymes, responsible for methyl transfer from AdoMet to the N1 position of the G37 base to synthesize m1G37 on tRNA. The methylated m1G37 is on the 3?-side of the anticodon, and it is necessary for suppressing tRNA frameshifting during protein synthesis on the ribosome TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism. The Mg2+ dependence is important for regulating Mg2+ transport to Salmonella for survival of the pathogen in the host cell. The trefoil knot of TrmD is required for the catalytic mechanism in three ways. Synthesis of m1G37-tRNA by TrmD is a posttranscriptional event
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physiological function
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the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, TrmD is required for growth in several bacterial species, including Escherichia coli and Salmonella
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physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
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physiological function
-
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
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physiological function
-
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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physiological function
-
he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
-
physiological function
-
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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physiological function
-
while the greatest majority of the tRNA modifying enzymes are nonessential for life, acting for example as a chaperone to modulate tRNA activity, a very small number of these enzymes are absolutely required for cell growth and survival. TrmD is an example of one of these essential enzymes, responsible for methyl transfer from AdoMet to the N1 position of the G37 base to synthesize m1G37 on tRNA. The methylated m1G37 is on the 3?-side of the anticodon, and it is necessary for suppressing tRNA frameshifting during protein synthesis on the ribosome TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism. The Mg2+ dependence is important for regulating Mg2+ transport to Salmonella for survival of the pathogen in the host cell. The trefoil knot of TrmD is required for the catalytic mechanism in three ways. Synthesis of m1G37-tRNA by TrmD is a posttranscriptional event
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physiological function
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the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, TrmD is required for growth in several bacterial species, including Escherichia coli and Salmonella
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physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
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physiological function
-
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
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physiological function
-
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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physiological function
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the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, Trm5 is required for growth in the single-cell eukaryote Saccharomyces cerevisiae, where it provides the important role of preventing mis-charging of tRNA
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physiological function
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the m1G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome
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physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
-
physiological function
-
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
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physiological function
-
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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physiological function
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methylation of guanine at position 37 in RNA is critical for bacterial growth, as this reaction is essential for preventing reading frame shifts during translation and therefore for maintaining the fidelity of protein synthesis. This methylation is catalyzed by the tRNA (guanine37-N1)-methyltransferase (TrmD). TrmD uses S-adenosyl-l-methionine (SAM) as a cofactor and transfers the methyl group to the N1 atom of G37 in tRNA. Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) plays important roles in translation. and is critical for growth of Pseudomonas aeruginosa
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physiological function
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m1G37 tRNA methyltransferase TrmD catalyzes m1G formation at position 37 in many tRNA isoacceptors and is essential
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physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
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physiological function
-
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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physiological function
Trametes pubescens 927 / 4 GUTat10.1 / TREU927
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TRM5 is responsible for m1G37 formation, m1G37 formation in mitochondria is important for respiration, and TbTRM5 is important for mitochondrial protein synthesis and biogenesis. Mitochondrial TRM5 may be needed to mature unmethylated tRNAs that reach the mitochondria and that can pose a problem for translational fidelity, lack of import specificity between some fully matured and potentially defective tRNA species
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physiological function
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he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
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physiological function
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methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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additional information
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S-adenosyl-methionine-dependent m1G37-tRNA methyltransferases rapidly screen tRNA by direct recognition of G37 in order to monitor the global state of m1G37-tRNA
additional information
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S-adenosyl-methionine-dependent m1G37-tRNA methyltransferases rapidly screen tRNA by direct recognition of G37 in order to monitor the global state of m1G37-tRNA
additional information
active-site structure and overall structure analysis, molecular modeling using structure PdB ID 2ZZN, overview
additional information
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active-site structure and overall structure analysis, molecular modeling using structure PdB ID 2ZZN, overview
additional information
in the cross-subunit active site, S-adenosyl-L-methionine is bound to the trefoil knot fold in the N-terminal domain, whereas the target G37 is predicted to bind to the flexible linker
additional information
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in the cross-subunit active site, S-adenosyl-L-methionine is bound to the trefoil knot fold in the N-terminal domain, whereas the target G37 is predicted to bind to the flexible linker
additional information
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three-dimensional enzyme model, overview
additional information
active site structure in complex with S-adenosyl-L-methionine, overview
additional information
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active site structure in complex with S-adenosyl-L-methionine, overview
additional information
Aquifex aeolicus TrmD can methylate G37 in the A36G37 sequence, showing that purine36 is a positive determinant for the TrmD. Formation of a disulfide bond between the two subunits stabilizes the dimer structure of Aquifex aeolicus TrmD and is required for enzymatic activity at high temperatures
additional information
backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa and secondary structure analysis
additional information
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backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa and secondary structure analysis
additional information
codon-specific translation in Mg2+ homeostasis, overview. Mg2+ homeostasis in Salmonella is maintained by the membrane-bound two-component system PhoPQ sensing of the external low Mg2+, which activates transcription of the major transporter gene mgtA. Transcription of mgtA is determined by ribosomal translation of the 5'-leader ORF, which contains several m1G37-dependent Pro codons
additional information
enzyme structure comparisons
additional information
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enzyme structure comparisons
additional information
evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
additional information
evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
additional information
evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
additional information
evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
additional information
structure comparison of the Pyrococcus abyssii Trm5a enzyme structure (PDB IDs 5HJJ and 5WT1) with the structure of its orthologue Trm5b (MjTrm5b, PDB IDs 2YX1 and 3AY0) from Methanococcus jannaschii, overview
additional information
structure comparison of the Pyrococcus abyssii Trm5a enzyme structure (PDB IDs 5HJJ and 5WT1) with the structure of its orthologue Trm5b (MjTrm5b, PDB IDs 2YX1 and 3AY0) from Methanococcus jannaschii, overview
additional information
the m1G37 methylation by TrmD does not need any other prior modification, aminoacylation, or even CCA addition to tRNA. Transient nature of Mg2+ is consistent with the proposed catalytic mechanism involving G37-tRNA. In this mechanism, D169 is the general base to abstract the N1 proton from G37, while the deprotonation is accompanied by developing electron density on the O6 of G37. The developing negative charge on O6 of G37 is stabilized through coordination with Mg2+ and by hydrogen-bond interaction with the side chain of R154. The charge stabilization of O6 in turn facilitates Mg2+ to coordinate with the general base D169 and to help it to align more properly for proton abstraction. The activated N1 nucleophile is then poised for nucleophilic attack on the sulfonium center of AdoMet, resulting in synthesis of m1G37-tRNA and release of AdoHcy. The rate-limiting step is assigned to the action of D169, rather than to the protonation of the leaving group, due to the importance of D169 and the increase of activity as the proton concentration is lowered
additional information
the m1G37 methylation by TrmD does not need any other prior modification, aminoacylation, or even CCA addition to tRNA. Transient nature of Mg2+ is consistent with the proposed catalytic mechanism involving G37-tRNA. In this mechanism, D169 is the general base to abstract the N1 proton from G37, while the deprotonation is accompanied by developing electron density on the O6 of G37. The developing negative charge on O6 of G37 is stabilized through coordination with Mg2+ and by hydrogen-bond interaction with the side chain of R154. The charge stabilization of O6 in turn facilitates Mg2+ to coordinate with the general base D169 and to help it to align more properly for proton abstraction. The activated N1 nucleophile is then poised for nucleophilic attack on the sulfonium center of AdoMet, resulting in synthesis of m1G37-tRNA and release of AdoHcy. The rate-limiting step is assigned to the action of D169, rather than to the protonation of the leaving group, due to the importance of D169 and the increase of activity as the proton concentration is lowered
additional information
the m1G37 methylation by TrmD does not need any other prior modification, aminoacylation, or even CCA addition to tRNA. Transient nature of Mg2+ is consistent with the proposed catalytic mechanism involving G37-tRNA. In this mechanism, D169 is the general base to abstract the N1 proton from G37, while the deprotonation is accompanied by developing electron density on the O6 of G37. The developing negative charge on O6 of G37 is stabilized through coordination with Mg2+ and by hydrogen-bond interaction with the side chain of R154. The charge stabilization of O6 in turn facilitates Mg2+ to coordinate with the general base D169 and to help it to align more properly for proton abstraction. The activated N1 nucleophile is then poised for nucleophilic attack on the sulfonium center of AdoMet, resulting in synthesis of m1G37-tRNA and release of AdoHcy. The rate-limiting step is assigned to the action of D169, rather than to the protonation of the leaving group, due to the importance of D169 and the increase of activity as the proton concentration is lowered
additional information
the m1G37 methylation by TrmD does not need any other prior modification, aminoacylation, or even CCA addition to tRNA. Transient nature of Mg2+ is consistent with the proposed catalytic mechanism involving G37-tRNA. In this mechanism, D169 is the general base to abstract the N1 proton from G37, while the deprotonation is accompanied by developing electron density on the O6 of G37. The developing negative charge on O6 of G37 is stabilized through coordination with Mg2+ and by hydrogen-bond interaction with the side chain of R154. The charge stabilization of O6 in turn facilitates Mg2+ to coordinate with the general base D169 and to help it to align more properly for proton abstraction. The activated N1 nucleophile is then poised for nucleophilic attack on the sulfonium center of AdoMet, resulting in synthesis of m1G37-tRNA and release of AdoHcy. The rate-limiting step is assigned to the action of D169, rather than to the protonation of the leaving group, due to the importance of D169 and the increase of activity as the proton concentration is lowered
additional information
the N-terminal domain (NTD) contains the S-adenosyl-L-methionine (SAM) binding region, this domain binds to SAM, S-adenosyl-L-homocysteine (SAH), and active-site inhibitors such as the SAM analogue sinefungin. Metabolites such as SAM, SAH and MTA enhance the thermostability of NTD by increasing its melting temperature (Tm), dynamics and ligand binding of NTD
additional information
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the N-terminal domain (NTD) contains the S-adenosyl-L-methionine (SAM) binding region, this domain binds to SAM, S-adenosyl-L-homocysteine (SAH), and active-site inhibitors such as the SAM analogue sinefungin. Metabolites such as SAM, SAH and MTA enhance the thermostability of NTD by increasing its melting temperature (Tm), dynamics and ligand binding of NTD
additional information
the structurally constrained TrmD knot is required for its catalytic activity. The TrmD knot has complex internal movements that respond to AdoMet binding and signaling. Most of the signaling propagates the free energy of AdoMet binding to stabilize tRNA binding and to assemble the active site. Principles of knots as an organized structure that captures the free energies of substrate binding to facilitate catalysis, overview
additional information
Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structure of D2 shares homology with that of TYW2, the tRNA-wybutosine (yW) synthesizing enzyme-2. D3 corresponds to the Rossmann-fold domain containing the AdoMet binding site, and is conserved among the class-I MTases. The D2-D3 fragment alone possesses methyl-transfer activity comparable to that of the full-length enzyme, although the presence of D1 lowers and enhances the KM and kcat values (the Michaelis and catalytic rate constants, respectively, in the Michaelis-Menten equation) for tRNA, respectively, as compared to the D2-D3 fragment. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
additional information
Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structures of Pyrococcus abyssi D1 and D2-D3 are similar to those of Methanocaldococcus jannaschii Trm5. The D1 of Pyrococcus abyssi Trm5a behaves independently from D2-D3, as suggested by the fluorescence resonance energy transfer (FRET) analysis. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
additional information
TrmD catalytic mechanism, overview. PaTrmD catalyzes the formation of m1G37 in tRNA by a ternary-complex mechanism in which tRNA and S-adenosyl-L-methionine can bind the protein independently. PaTrmD shares functionally important amino acid residues involved in cofactor binding (Ser93-Gly96, Gly118, Ile123, Ser137, Gly145), tRNA binding (Gly60, Gly64, Ser203-His206) and catalytic activity (Asp54, Arg159, and Asp174). Conformational changes are required to form a ternary complex with tRNA. PaTrmD catalyzes only the m1G modification in PA14 tRNAs that possess a G36G37 motif, the G36G37 motif is a substrate of PaTrmD. PaTrmD catalyzes m1G formation in synthetic tRNA substrates indicating that PaTrmD can use G36G37 containing tRNAs without other modifications as substrates. Enzyme structure modelling, overview
additional information
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TrmD catalytic mechanism, overview. PaTrmD catalyzes the formation of m1G37 in tRNA by a ternary-complex mechanism in which tRNA and S-adenosyl-L-methionine can bind the protein independently. PaTrmD shares functionally important amino acid residues involved in cofactor binding (Ser93-Gly96, Gly118, Ile123, Ser137, Gly145), tRNA binding (Gly60, Gly64, Ser203-His206) and catalytic activity (Asp54, Arg159, and Asp174). Conformational changes are required to form a ternary complex with tRNA. PaTrmD catalyzes only the m1G modification in PA14 tRNAs that possess a G36G37 motif, the G36G37 motif is a substrate of PaTrmD. PaTrmD catalyzes m1G formation in synthetic tRNA substrates indicating that PaTrmD can use G36G37 containing tRNAs without other modifications as substrates. Enzyme structure modelling, overview
additional information
TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview
additional information
TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview
additional information
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Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structures of Pyrococcus abyssi D1 and D2-D3 are similar to those of Methanocaldococcus jannaschii Trm5. The D1 of Pyrococcus abyssi Trm5a behaves independently from D2-D3, as suggested by the fluorescence resonance energy transfer (FRET) analysis. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
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additional information
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the m1G37 methylation by TrmD does not need any other prior modification, aminoacylation, or even CCA addition to tRNA. Transient nature of Mg2+ is consistent with the proposed catalytic mechanism involving G37-tRNA. In this mechanism, D169 is the general base to abstract the N1 proton from G37, while the deprotonation is accompanied by developing electron density on the O6 of G37. The developing negative charge on O6 of G37 is stabilized through coordination with Mg2+ and by hydrogen-bond interaction with the side chain of R154. The charge stabilization of O6 in turn facilitates Mg2+ to coordinate with the general base D169 and to help it to align more properly for proton abstraction. The activated N1 nucleophile is then poised for nucleophilic attack on the sulfonium center of AdoMet, resulting in synthesis of m1G37-tRNA and release of AdoHcy. The rate-limiting step is assigned to the action of D169, rather than to the protonation of the leaving group, due to the importance of D169 and the increase of activity as the proton concentration is lowered
-
additional information
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codon-specific translation in Mg2+ homeostasis, overview. Mg2+ homeostasis in Salmonella is maintained by the membrane-bound two-component system PhoPQ sensing of the external low Mg2+, which activates transcription of the major transporter gene mgtA. Transcription of mgtA is determined by ribosomal translation of the 5'-leader ORF, which contains several m1G37-dependent Pro codons
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additional information
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Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structure of D2 shares homology with that of TYW2, the tRNA-wybutosine (yW) synthesizing enzyme-2. D3 corresponds to the Rossmann-fold domain containing the AdoMet binding site, and is conserved among the class-I MTases. The D2-D3 fragment alone possesses methyl-transfer activity comparable to that of the full-length enzyme, although the presence of D1 lowers and enhances the KM and kcat values (the Michaelis and catalytic rate constants, respectively, in the Michaelis-Menten equation) for tRNA, respectively, as compared to the D2-D3 fragment. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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additional information
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TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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additional information
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structure comparison of the Pyrococcus abyssii Trm5a enzyme structure (PDB IDs 5HJJ and 5WT1) with the structure of its orthologue Trm5b (MjTrm5b, PDB IDs 2YX1 and 3AY0) from Methanococcus jannaschii, overview
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additional information
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Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structure of D2 shares homology with that of TYW2, the tRNA-wybutosine (yW) synthesizing enzyme-2. D3 corresponds to the Rossmann-fold domain containing the AdoMet binding site, and is conserved among the class-I MTases. The D2-D3 fragment alone possesses methyl-transfer activity comparable to that of the full-length enzyme, although the presence of D1 lowers and enhances the KM and kcat values (the Michaelis and catalytic rate constants, respectively, in the Michaelis-Menten equation) for tRNA, respectively, as compared to the D2-D3 fragment. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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additional information
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the m1G37 methylation by TrmD does not need any other prior modification, aminoacylation, or even CCA addition to tRNA. Transient nature of Mg2+ is consistent with the proposed catalytic mechanism involving G37-tRNA. In this mechanism, D169 is the general base to abstract the N1 proton from G37, while the deprotonation is accompanied by developing electron density on the O6 of G37. The developing negative charge on O6 of G37 is stabilized through coordination with Mg2+ and by hydrogen-bond interaction with the side chain of R154. The charge stabilization of O6 in turn facilitates Mg2+ to coordinate with the general base D169 and to help it to align more properly for proton abstraction. The activated N1 nucleophile is then poised for nucleophilic attack on the sulfonium center of AdoMet, resulting in synthesis of m1G37-tRNA and release of AdoHcy. The rate-limiting step is assigned to the action of D169, rather than to the protonation of the leaving group, due to the importance of D169 and the increase of activity as the proton concentration is lowered
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additional information
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codon-specific translation in Mg2+ homeostasis, overview. Mg2+ homeostasis in Salmonella is maintained by the membrane-bound two-component system PhoPQ sensing of the external low Mg2+, which activates transcription of the major transporter gene mgtA. Transcription of mgtA is determined by ribosomal translation of the 5'-leader ORF, which contains several m1G37-dependent Pro codons
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additional information
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Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structure of D2 shares homology with that of TYW2, the tRNA-wybutosine (yW) synthesizing enzyme-2. D3 corresponds to the Rossmann-fold domain containing the AdoMet binding site, and is conserved among the class-I MTases. The D2-D3 fragment alone possesses methyl-transfer activity comparable to that of the full-length enzyme, although the presence of D1 lowers and enhances the KM and kcat values (the Michaelis and catalytic rate constants, respectively, in the Michaelis-Menten equation) for tRNA, respectively, as compared to the D2-D3 fragment. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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additional information
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Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structure of D2 shares homology with that of TYW2, the tRNA-wybutosine (yW) synthesizing enzyme-2. D3 corresponds to the Rossmann-fold domain containing the AdoMet binding site, and is conserved among the class-I MTases. The D2-D3 fragment alone possesses methyl-transfer activity comparable to that of the full-length enzyme, although the presence of D1 lowers and enhances the KM and kcat values (the Michaelis and catalytic rate constants, respectively, in the Michaelis-Menten equation) for tRNA, respectively, as compared to the D2-D3 fragment. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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additional information
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TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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additional information
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TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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additional information
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active site structure in complex with S-adenosyl-L-methionine, overview
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additional information
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backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa and secondary structure analysis
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additional information
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the N-terminal domain (NTD) contains the S-adenosyl-L-methionine (SAM) binding region, this domain binds to SAM, S-adenosyl-L-homocysteine (SAH), and active-site inhibitors such as the SAM analogue sinefungin. Metabolites such as SAM, SAH and MTA enhance the thermostability of NTD by increasing its melting temperature (Tm), dynamics and ligand binding of NTD
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additional information
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TrmD catalytic mechanism, overview. PaTrmD catalyzes the formation of m1G37 in tRNA by a ternary-complex mechanism in which tRNA and S-adenosyl-L-methionine can bind the protein independently. PaTrmD shares functionally important amino acid residues involved in cofactor binding (Ser93-Gly96, Gly118, Ile123, Ser137, Gly145), tRNA binding (Gly60, Gly64, Ser203-His206) and catalytic activity (Asp54, Arg159, and Asp174). Conformational changes are required to form a ternary complex with tRNA. PaTrmD catalyzes only the m1G modification in PA14 tRNAs that possess a G36G37 motif, the G36G37 motif is a substrate of PaTrmD. PaTrmD catalyzes m1G formation in synthetic tRNA substrates indicating that PaTrmD can use G36G37 containing tRNAs without other modifications as substrates. Enzyme structure modelling, overview
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additional information
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TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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additional information
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Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structure of D2 shares homology with that of TYW2, the tRNA-wybutosine (yW) synthesizing enzyme-2. D3 corresponds to the Rossmann-fold domain containing the AdoMet binding site, and is conserved among the class-I MTases. The D2-D3 fragment alone possesses methyl-transfer activity comparable to that of the full-length enzyme, although the presence of D1 lowers and enhances the KM and kcat values (the Michaelis and catalytic rate constants, respectively, in the Michaelis-Menten equation) for tRNA, respectively, as compared to the D2-D3 fragment. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures
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additional information
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evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
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