The Enzyme Database

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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 2.5.1.114     
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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