The Enzyme Database

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EC 1.14.11.42     
Accepted name: tRNAPhe (7-(3-amino-3-carboxypropyl)wyosine37-C2)-hydroxylase
Reaction: 7-(3-amino-3-carboxypropyl)wyosine37 in tRNAPhe + 2-oxoglutarate + O2 = 7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine37 in tRNAPhe + succinate + CO2
For diagram of wyosine biosynthesis, click here
Glossary: 7-(3-amino-3-carboxypropyl)wyosine = 7-[(3S)-3-amino-3-carboxypropyl]-4,6-dimethyl-3-(-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine = 4-[4,6-dimethyl-9-oxo-3-(-D-ribofuranosyl)-4,9-dihydro-3H-imidazo[1,2-a]purin-7-yl]-L-threonine
Other name(s): TYW5; tRNA yW-synthesizing enzyme 5
Systematic name: tRNAPhe 7-(3-amino-3-carboxypropyl)wyosine37,2-oxoglutarate:oxygen oxidoreductase (2-hydroxylating)
Comments: Requires Fe2+. The enzyme is not active with wybutosine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Noma, A., Ishitani, R., Kato, M., Nagao, A., Nureki, O. and Suzuki, T. Expanding role of the jumonji C domain as an RNA hydroxylase. J. Biol. Chem. 285 (2010) 34503–34507. [DOI] [PMID: 20739293]
2.  Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576–1585. [DOI] [PMID: 20972222]
[EC 1.14.11.42 created 2013]
 
 
EC 2.1.1.228     
Accepted name: tRNA (guanine37-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
For diagram of wyosine biosynthesis, click here
Other name(s): TrmD; tRNA (m1G37) methyltransferase; transfer RNA (m1G37) methyltransferase; Trm5p; TRMT5; tRNA-(N1G37) methyltransferase; MJ0883 (gene name)
Systematic name: S-adenosyl-L-methionine:tRNA (guanine37-N1)-methyltransferase
Comments: This enzyme is important for the maintenance of the correct reading frame during translation. Unlike TrmD from Escherichia coli, which recognizes the G36pG37 motif preferentially, the human enzyme (encoded by TRMT5) also methylates inosine at position 37 [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Takeda, H., Toyooka, T., Ikeuchi, Y., Yokobori, S., Okadome, K., Takano, F., Oshima, T., Suzuki, T., Endo, Y. and Hori, H. The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus. Genes Cells 11 (2006) 1353–1365. [DOI] [PMID: 17121543]
2.  Lee, C., Kramer, G., Graham, D.E. and Appling, D.R. Yeast mitochondrial initiator tRNA is methylated at guanosine 37 by the Trm5-encoded tRNA (guanine-N1-)-methyltransferase. J. Biol. Chem. 282 (2007) 27744–27753. [DOI] [PMID: 17652090]
3.  O'Dwyer, K., Watts, J.M., Biswas, S., Ambrad, J., Barber, M., Brule, H., Petit, C., Holmes, D.J., Zalacain, M. and Holmes, W.M. Characterization of Streptococcus pneumoniae TrmD, a tRNA methyltransferase essential for growth. J. Bacteriol. 186 (2004) 2346–2354. [DOI] [PMID: 15060037]
4.  Brule, H., Elliott, M., Redlak, M., Zehner, Z.E. and Holmes, W.M. Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein. Biochemistry 43 (2004) 9243–9255. [DOI] [PMID: 15248782]
5.  Goto-Ito, S., Ito, T., Ishii, R., Muto, Y., Bessho, Y. and Yokoyama, S. Crystal structure of archaeal RNA(m1G37)methyltransferase aTrm5. Proteins 72 (2008) 1274–1289. [DOI] [PMID: 18384044]
6.  Ahn, H.J., Kim, H.W., Yoon, H.J., Lee, B.I., Suh, S.W. and Yang, J.K. Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition. EMBO J. 22 (2003) 2593–2603. [DOI] [PMID: 12773376]
[EC 2.1.1.228 created 2011 (EC 2.1.1.31 created 1971, part transferred 2011 to EC 2.1.1.228)]
 
 
EC 2.1.1.282     
Accepted name: tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe = S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-{(3S)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW3 (gene name); tRNA-yW synthesizing enzyme-3
Systematic name: S-adenosyl-L-methionine:tRNAPhe 7-[(3S)-(3-amino-3-carboxypropyl)-4-demethylwyosine-N4]-methyltransferase
Comments: The enzyme is involved in the biosynthesis of hypermodified tricyclic bases found at position 37 of certain tRNAs. These modifications are important for translational reading-frame maintenance. The enzyme is found in all eukaryotes and in some archaea, but not in bacteria. The eukaryotic enzyme is involved in the biosynthesis of wybutosine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]
[EC 2.1.1.282 created 2013, modified 2014]
 
 
EC 2.1.1.290     
Accepted name: tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-3-amino-3-carboxypropyl]wyosine37 in tRNAPhe = S-adenosyl-L-homocysteine + 7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-[(3S)-3-(methoxycarbonyl)-3-(methoxycarbonylamino)propyl]-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW4 (ambiguous); tRNA-yW synthesizing enzyme-4 (ambiguous)
Systematic name: S-adenosyl-L-methionine:tRNAPhe {7-[(3S)-3-amino-3-carboxypropyl]wyosine37-O}-methyltransferase
Comments: The enzyme is found only in eukaryotes, where it is involved in the biosynthesis of wybutosine, a hypermodified tricyclic base found at position 37 of certain tRNAs. The modification is important for translational reading-frame maintenance. In some species that produce hydroxywybutosine the enzyme uses 7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine37 in tRNAPhe as substrate. The enzyme also has the activity of EC 2.3.1.231, tRNAPhe 7-[(3S)-4-methoxy-(3-amino-3-carboxypropyl)wyosine37-O]-carbonyltransferase [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]
2.  Suzuki, Y., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 37 (2009) 2910–2925. [DOI] [PMID: 19287006]
3.  Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576–1585. [DOI] [PMID: 20972222]
[EC 2.1.1.290 created 2013]
 
 
EC 2.3.1.231     
Accepted name: tRNAPhe {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methoxycarbonyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe + CO2 = S-adenosyl-L-homocysteine + wybutosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-{(3S)-3-(methoxycarbonyl)-3-(methoxycarbonylamino)propyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW4 (ambiguous); tRNA-yW synthesizing enzyme-4 (ambiguous)
Systematic name: S-adenosyl-L-methionine:tRNAPhe {7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methyltransferase (carbon dioxide-adding)
Comments: The enzyme is found only in eukaryotes, where it is involved in the biosynthesis of wybutosine, a hypermodified tricyclic base found at position 37 of certain tRNAs. The modification is important for translational reading-frame maintenance. In some species that produce hydroxywybutosine the enzyme uses 7-[2-hydroxy-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe as substrate. The enzyme also has the activity of EC 2.1.1.290, tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]
2.  Suzuki, Y., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 37 (2009) 2910–2925. [DOI] [PMID: 19287006]
3.  Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576–1585. [DOI] [PMID: 20972222]
[EC 2.3.1.231 created 2013]
 
 
EC 2.5.1.114     
Accepted name: tRNAPhe (4-demethylwyosine37-C7) aminocarboxypropyltransferase
Reaction: S-adenosyl-L-methionine + 4-demethylwyosine37 in tRNAPhe = S-methyl-5′-thioadenosine + 7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: 4-demethylwyosine = imG-14 = 6-methyl-3-(β-D-ribofuranosyl)-3,5-dihydro-9H-imidazo[1,2-a]purin-9-one
7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine = yW-89
Other name(s): TYW2; tRNA-yW synthesizing enzyme-2; TRM12 (gene name); taw2 (gene name)
Systematic name: S-adenosyl-L-methionine:tRNAPhe (4-demethylwyosine37-C7)-[(3S)-3-amino-3-carboxypropyl]transferase
Comments: The enzyme, which is found in all eukaryotes and in the majority of Euryarchaeota (but not in the Crenarchaeota), is involved in the hypermodification of the guanine nucleoside at position 37 of tRNA leading to formation of assorted wye bases. This modification is essential for translational reading-frame maintenance. The eukaryotic enzyme is involved in biosynthesis of the tricyclic base wybutosine, which is found only in tRNAPhe.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Umitsu, M., Nishimasu, H., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc. Natl. Acad. Sci. USA 106 (2009) 15616–15621. [DOI] [PMID: 19717466]
2.  Rodriguez, V., Vasudevan, S., Noma, A., Carlson, B.A., Green, J.E., Suzuki, T. and Chandrasekharappa, S.C. Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PLoS One 7:e39297 (2012). [DOI] [PMID: 22761755]
3.  de Crecy-Lagard, V., Brochier-Armanet, C., Urbonavicius, J., Fernandez, B., Phillips, G., Lyons, B., Noma, A., Alvarez, S., Droogmans, L., Armengaud, J. and Grosjean, H. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol. Biol. Evol. 27 (2010) 2062–2077. [DOI] [PMID: 20382657]
[EC 2.5.1.114 created 2013]
 
 
EC 4.1.3.44     
Accepted name: tRNA 4-demethylwyosine synthase (AdoMet-dependent)
Reaction: N1-methylguanine37 in tRNAPhe + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine37 in tRNAPhe + L-methionine + 5′-deoxyadenosine + CO2 + H2O
For diagram of wyosine biosynthesis, click here
Glossary: 4-demethylwyosine = imG-14 = 6-methyl-3-(β-D-ribofuranosyl)-3,5-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW1
Systematic name: tRNAPhe N1-methylguanine,pyruvate acetaldehyde-lyase (tRNAPhe 4-demethylwyosine-forming, decarboxylating, dehydrating)
Comments: This enzyme, which is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes, binds two [4Fe-4S] clusters [3,4]. Carbons C2 and C3 from pyruvate are incorporated into 4-demethylwyosine [3]. The enzyme is found in eukaryotes where it is part of the pathway for wybutosine synthesis, and in archaea, where it is involved in the biosynthesis of archaeal wye bases, such as wyosine, isowyosine, and methylwyosine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Goto-Ito, S., Ishii, R., Ito, T., Shibata, R., Fusatomi, E., Sekine, S.I., Bessho, Y. and Yokoyama, S. Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 63 (2007) 1059–1068. [DOI] [PMID: 17881823]
2.  Suzuki, Y., Noma, A., Suzuki, T., Senda, M., Senda, T., Ishitani, R. and Nureki, O. Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA. J. Mol. Biol. 372 (2007) 1204–1214. [DOI] [PMID: 17727881]
3.  Young, A.P. and Bandarian, V. Pyruvate is the source of the two carbons that are required for formation of the imidazoline ring of 4-demethylwyosine. Biochemistry 50 (2011) 10573–10575. [DOI] [PMID: 22026549]
4.  Perche-Letuvée, P., Kathirvelu, V., Berggren, G., Clemancey, M., Latour, J.M., Maurel, V., Douki, T., Armengaud, J., Mulliez, E., Fontecave, M., Garcia-Serres, R., Gambarelli, S. and Atta, M. 4-Demethylwyosine synthase from Pyrococcus abyssi is a radical-S-adenosyl-L-methionine enzyme with an additional [4Fe-4S]2+ cluster that interacts with the pyruvate co-substrate. J. Biol. Chem. 287 (2012) 41174–41185. [DOI] [PMID: 23043105]
[EC 4.1.3.44 created 2013]
 
 


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