Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary extracted from

  • Goto-Ito, S.; Ito, T.; Yokoyama, S.
    Trm5 and TrmD two enzymes from distinct origins catalyze the identical tRNA modification, m1G37 (2017), Biomolecules, 7, 32 .
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.1.1.228 TrmD-tRNA-sinefungin complex, crystal structure determination and analysis. In this complex structure, one TrmD homodimer is complexed with one tRNA molecule, and each TrmD monomer binds a sinefungin molecule. This binding mode is consistent with the previously reported biochemical analysis. When the substrate tRNA interacts with the catalytic pocket of subunit A, the NTDs of subunits A and B, and the neighboring CTD of subunit B, contact the tRNA. The interdomain linker of subunit B forms a helix upon tRNA binding, and participates in the interaction with the substrate tRNA Haemophilus influenzae

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.1.1.228 additional information
-
 additional information Michaelis-Menten kinetic analysis Methanocaldococcus jannaschii
2.1.1.228 additional information
-
 additional information Michaelis-Menten kinetic analysis Haemophilus influenzae
2.1.1.228 additional information
-
 additional information Michaelis-Menten kinetic analysis Escherichia coli
2.1.1.228 additional information
-
 additional information Michaelis-Menten kinetic analysis Pyrococcus abyssi

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Methanocaldococcus jannaschii
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Haemophilus influenzae
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Escherichia coli
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Pyrococcus abyssi
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Pyrococcus abyssi Orsay
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Methanocaldococcus jannaschii NBRC 100440
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Haemophilus influenzae RD
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Methanocaldococcus jannaschii DSM 2661
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Methanocaldococcus jannaschii ATCC 43067
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Methanocaldococcus jannaschii JAL-1
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Haemophilus influenzae DSM 11121
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Haemophilus influenzae KW20
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Haemophilus influenzae ATCC 51907
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Methanocaldococcus jannaschii JCM 10045
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + wyosine37 in tRNAPhe Pyrococcus abyssi
-
 S-adenosyl-L-homocysteine + N1-methylwyosine37 in tRNAPhe
-
 ?
2.1.1.228 S-adenosyl-L-methionine + wyosine37 in tRNAPhe Pyrococcus abyssi Orsay
-
 S-adenosyl-L-homocysteine + N1-methylwyosine37 in tRNAPhe
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.228 Escherichia coli P0A873
-
-
2.1.1.228 Haemophilus influenzae P43912
-
-
2.1.1.228 Haemophilus influenzae ATCC 51907 P43912
-
-
2.1.1.228 Haemophilus influenzae DSM 11121 P43912
-
-
2.1.1.228 Haemophilus influenzae KW20 P43912
-
-
2.1.1.228 Haemophilus influenzae RD P43912
-
-
2.1.1.228 Methanocaldococcus jannaschii Q58293 i.e. Methanococcus jannaschii
-
2.1.1.228 Methanocaldococcus jannaschii ATCC 43067 Q58293 i.e. Methanococcus jannaschii
-
2.1.1.228 Methanocaldococcus jannaschii DSM 2661 Q58293 i.e. Methanococcus jannaschii
-
2.1.1.228 Methanocaldococcus jannaschii JAL-1 Q58293 i.e. Methanococcus jannaschii
-
2.1.1.228 Methanocaldococcus jannaschii JCM 10045 Q58293 i.e. Methanococcus jannaschii
-
2.1.1.228 Methanocaldococcus jannaschii NBRC 100440 Q58293 i.e. Methanococcus jannaschii
-
2.1.1.228 Pyrococcus abyssi Q9V2G1
-
-
2.1.1.228 Pyrococcus abyssi Orsay Q9V2G1
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.228 additional information proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37 Haemophilus influenzae ?
-
-
2.1.1.228 additional information proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37 Escherichia coli ?
-
-
2.1.1.228 additional information tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA Methanocaldococcus jannaschii ?
-
-
2.1.1.228 additional information tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA Pyrococcus abyssi ?
-
-
2.1.1.228 additional information tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA Pyrococcus abyssi Orsay ?
-
-
2.1.1.228 additional information tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA Methanocaldococcus jannaschii NBRC 100440 ?
-
-
2.1.1.228 additional information proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37 Haemophilus influenzae RD ?
-
-
2.1.1.228 additional information tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA Methanocaldococcus jannaschii DSM 2661 ?
-
-
2.1.1.228 additional information tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA Methanocaldococcus jannaschii ATCC 43067 ?
-
-
2.1.1.228 additional information tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA Methanocaldococcus jannaschii JAL-1 ?
-
-
2.1.1.228 additional information proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37 Haemophilus influenzae DSM 11121 ?
-
-
2.1.1.228 additional information proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37 Haemophilus influenzae KW20 ?
-
-
2.1.1.228 additional information proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37 Haemophilus influenzae ATCC 51907 ?
-
-
2.1.1.228 additional information tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA Methanocaldococcus jannaschii JCM 10045 ?
-
-
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Methanocaldococcus jannaschii S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Haemophilus influenzae S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Escherichia coli S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Pyrococcus abyssi S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Pyrococcus abyssi Orsay S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Methanocaldococcus jannaschii NBRC 100440 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Haemophilus influenzae RD S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Methanocaldococcus jannaschii DSM 2661 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Methanocaldococcus jannaschii ATCC 43067 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Methanocaldococcus jannaschii JAL-1 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Haemophilus influenzae DSM 11121 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Haemophilus influenzae KW20 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Haemophilus influenzae ATCC 51907 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Methanocaldococcus jannaschii JCM 10045 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + wyosine37 in tRNAPhe
-
 Pyrococcus abyssi S-adenosyl-L-homocysteine + N1-methylwyosine37 in tRNAPhe
-
 ?
2.1.1.228 S-adenosyl-L-methionine + wyosine37 in tRNAPhe
-
 Pyrococcus abyssi Orsay S-adenosyl-L-homocysteine + N1-methylwyosine37 in tRNAPhe
-
 ?

Subunits

EC Number Subunits Comment Organism
2.1.1.228 dimer deep-trefoil knot structure Haemophilus influenzae
2.1.1.228 dimer deep-trefoil knot structure Escherichia coli
2.1.1.228 monomer Rossmann fold structure Methanocaldococcus jannaschii
2.1.1.228 monomer Rossmann fold structure Pyrococcus abyssi

Synonyms

EC Number Synonyms Comment Organism
2.1.1.228 TAW22
-
 Pyrococcus abyssi
2.1.1.228 TRM5
-
 Methanocaldococcus jannaschii
2.1.1.228 Trm5a
-
 Pyrococcus abyssi
2.1.1.228 trm5b
-
 Methanocaldococcus jannaschii
2.1.1.228 TrmD
-
 Haemophilus influenzae
2.1.1.228 TrmD
-
 Escherichia coli
2.1.1.228 tRNA methyltransferase 5
-
 Methanocaldococcus jannaschii
2.1.1.228 tRNA methyltransferase 5
-
 Pyrococcus abyssi
2.1.1.228 tRNA methyltransferase D
-
 Haemophilus influenzae
2.1.1.228 tRNA methyltransferase D
-
 Escherichia coli

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.228 S-adenosyl-L-methionine
-
 Methanocaldococcus jannaschii
2.1.1.228 S-adenosyl-L-methionine
-
 Haemophilus influenzae
2.1.1.228 S-adenosyl-L-methionine
-
 Escherichia coli
2.1.1.228 S-adenosyl-L-methionine
-
 Pyrococcus abyssi

General Information

EC Number General Information Comment Organism
2.1.1.228 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 Haemophilus influenzae
2.1.1.228 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. Escherichia coli
2.1.1.228 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 Methanocaldococcus jannaschii
2.1.1.228 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 Pyrococcus abyssi
2.1.1.228 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 Methanocaldococcus jannaschii
2.1.1.228 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 Pyrococcus abyssi
2.1.1.228 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 Methanocaldococcus jannaschii
2.1.1.228 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 Pyrococcus abyssi
2.1.1.228 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 Haemophilus influenzae
2.1.1.228 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 Escherichia coli
2.1.1.228 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 Methanocaldococcus jannaschii
2.1.1.228 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 Haemophilus influenzae
2.1.1.228 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 Escherichia coli
2.1.1.228 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 Pyrococcus abyssi