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, PDB
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 2.1.1.290     
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, PDB
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, PDB
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]
 
 


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