The Enzyme Database

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EC 2.5.1.77      
Transferred entry: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase. Now EC 2.5.1.147, 5-amino-6-(D-ribitylamino)uracilL-tyrosine 4-methylphenol transferase and EC 4.3.1.32, 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase.
[EC 2.5.1.77 created 2010, deleted 2018]
 
 
EC 2.5.1.78     
Accepted name: 6,7-dimethyl-8-ribityllumazine synthase
Reaction: 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
For diagram of riboflavin biosynthesis (late stages), click here and for mechanism, click here
Glossary: 5-amino-6-(D-ribitylamino)uracil = 5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione
6,7-dimethyl-8-(1-D-ribityl)lumazine = 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol
Other name(s): lumazine synthase; 6,7-dimethyl-8-ribityllumazine synthase 2; 6,7-dimethyl-8-ribityllumazine synthase 1; lumazine synthase 2; lumazine synthase 1; type I lumazine synthase; type II lumazine synthase; RIB4; MJ0303; RibH; Pbls; MbtLS; RibH1 protein; RibH2 protein; RibH1; RibH2
Systematic name: 5-amino-6-(D-ribitylamino)uracil butanedionetransferase
Comments: Involved in riboflavin biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kis, K., Volk, R. and Bacher, A. Biosynthesis of riboflavin. Studies on the reaction mechanism of 6,7-dimethyl-8-ribityllumazine synthase. Biochemistry 34 (1995) 2883–2892. [PMID: 7893702]
2.  Garcia-Ramirez, J.J., Santos, M.A. and Revuelta, J.L. The Saccharomyces cerevisiae RIB4 gene codes for 6,7-dimethyl-8-ribityllumazine synthase involved in riboflavin biosynthesis. Molecular characterization of the gene and purification of the encoded protein. J. Biol. Chem. 270 (1995) 23801–23807. [DOI] [PMID: 7559556]
3.  Bacher, A., Fischer, M., Kis, K., Kugelbrey, K., Mörtl, S., Scheuring, J., Weinkauf, S., Eberhardt, S., Schmidt-Bäse, K., Huber, R., Ritsert, K., Cushman, M., Ladenstein, R. Biosynthesis of riboflavin: structure and mechanism of lumazine synthase. Biochem. Soc. Trans. 24 (1996) 89–94. [PMID: 8674771]
4.  Mörtl, S., Fischer, M., Richter, G., Tack, J., Weinkauf, S. and Bacher, A. Biosynthesis of riboflavin. Lumazine synthase of Escherichia coli. J. Biol. Chem. 271 (1996) 33201–33207. [DOI] [PMID: 8969176]
5.  Bacher, A., Eberhardt, S., Fischer, M., Mortl, S., Kis, K., Kugelbrey, K., Scheuring, J. and Schott, K. Biosynthesis of riboflavin: lumazine synthase and riboflavin synthase. Methods Enzymol. 280 (1997) 389–399. [DOI] [PMID: 9211334]
6.  Goldbaum, F.A., Velikovsky, C.A., Baldi, P.C., Mortl, S., Bacher, A. and Fossati, C.A. The 18-kDa cytoplasmic protein of Brucella species - an antigen useful for diagnosis - is a lumazine synthase. J. Med. Microbiol. 48 (1999) 833–839. [DOI] [PMID: 10482294]
7.  Jordan, D.B., Bacot, K.O., Carlson, T.J., Kessel, M. and Viitanen, P.V. Plant riboflavin biosynthesis. Cloning, chloroplast localization, expression, purification, and partial characterization of spinach lumazine synthase. J. Biol. Chem. 274 (1999) 22114–22121. [DOI] [PMID: 10419541]
8.  Zhang, X., Meining, W., Fischer, M., Bacher, A. and Ladenstein, R. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 Å resolution: determinants of thermostability revealed from structural comparisons. J. Mol. Biol. 306 (2001) 1099–1114. [DOI] [PMID: 11237620]
9.  Fischer, M., Haase, I., Feicht, R., Richter, G., Gerhardt, S., Changeux, J.P., Huber, R. and Bacher, A. Biosynthesis of riboflavin: 6,7-dimethyl-8-ribityllumazine synthase of Schizosaccharomyces pombe. Eur. J. Biochem. 269 (2002) 519–526. [DOI] [PMID: 11856310]
10.  Cushman, M., Yang, D., Gerhardt, S., Huber, R., Fischer, M., Kis, K. and Bacher, A. Design, synthesis, and evaluation of 6-carboxyalkyl and 6-phosphonoxyalkyl derivatives of 7-oxo-8-ribitylaminolumazines as inhibitors of riboflavin synthase and lumazine synthase. J. Org. Chem. 67 (2002) 5807–5816. [DOI] [PMID: 12153285]
11.  Haase, I., Mortl, S., Kohler, P., Bacher, A. and Fischer, M. Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii. Eur. J. Biochem. 270 (2003) 1025–1032. [DOI] [PMID: 12603336]
12.  Morgunova, E., Meining, W., Illarionov, B., Haase, I., Jin, G., Bacher, A., Cushman, M., Fischer, M. and Ladenstein, R. Crystal structure of lumazine synthase from Mycobacterium tuberculosis as a target for rational drug design: binding mode of a new class of purinetrione inhibitors. Biochemistry 44 (2005) 2746–2758. [DOI] [PMID: 15723519]
13.  Morgunova, E., Saller, S., Haase, I., Cushman, M., Bacher, A., Fischer, M. and Ladenstein, R. Lumazine synthase from Candida albicans as an anti-fungal target enzyme: structural and biochemical basis for drug design. J. Biol. Chem. 282 (2007) 17231–17241. [DOI] [PMID: 17446177]
[EC 2.5.1.78 created 2010]
 
 
EC 2.5.1.147     
Accepted name: 5-amino-6-(D-ribitylamino)uracilL-tyrosine 4-hydroxyphenyl transferase
Reaction: 5-amino-6-(D-ribitylamino)uracil + L-tyrosine + S-adenosyl-L-methionine = 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil + 2-iminoacetate + L-methionine + 5′-deoxyadenosine
Glossary: 5-amino-6-(D-ribitylamino)uracil = 5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione
Other name(s): cofH (gene name); cbiF (gene name) (ambiguous)
Systematic name: 5-amino-6-(D-ribitylamino)uracil:L-tyrosine, 4-hydroxyphenyl transferase
Comments: The enzyme is involved in the production of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO), the precursor of the redox cofactor coenzyme F420, which is found in methanogens and in various actinobacteria. FO is also produced by some cyanobacteria and eukaryotes. The enzyme, which forms a complex with EC 4.3.1.32, 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, is a radical SAM enzyme that uses the 5′-deoxyadenosyl radical to initiate the reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Decamps, L., Philmus, B., Benjdia, A., White, R., Begley, T.P. and Berteau, O. Biosynthesis of F0, precursor of the F420 cofactor, requires a unique two radical-SAM domain enzyme and tyrosine as substrate. J. Am. Chem. Soc. 134 (2012) 18173–18176. [DOI] [PMID: 23072415]
2.  Philmus, B., Decamps, L., Berteau, O. and Begley, T.P. Biosynthetic versatility and coordinated action of 5′-deoxyadenosyl radicals in deazaflavin biosynthesis. J. Am. Chem. Soc. 137 (2015) 5406–5413. [DOI] [PMID: 25781338]
[EC 2.5.1.147 created 2010 as EC 2.5.1.77, part transferred 2018 to EC 2.5.1.147]
 
 
EC 3.1.3.104     
Accepted name: 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase
Reaction: 5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O = 5-amino-6-(D-ribitylamino)uracil + phosphate
Other name(s): 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5′-phosphate phosphatase
Systematic name: 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphohydrolase
Comments: Requires Mg2+. The enzyme, which is found in plants and bacteria, is part of a pathway for riboflavin biosynthesis. Most forms of the enzyme has a broad substrate specificity [1,3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Haase, I., Sarge, S., Illarionov, B., Laudert, D., Hohmann, H.P., Bacher, A. and Fischer, M. Enzymes from the haloacid dehalogenase (HAD) superfamily catalyse the elusive dephosphorylation step of riboflavin biosynthesis. ChemBioChem 14 (2013) 2272–2275. [DOI] [PMID: 24123841]
2.  London, N., Farelli, J.D., Brown, S.D., Liu, C., Huang, H., Korczynska, M., Al-Obaidi, N.F., Babbitt, P.C., Almo, S.C., Allen, K.N. and Shoichet, B.K. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry 54 (2015) 528–537. [DOI] [PMID: 25513739]
3.  Sarge, S., Haase, I., Illarionov, B., Laudert, D., Hohmann, H.P., Bacher, A. and Fischer, M. Catalysis of an essential step in vitamin B2 biosynthesis by a consortium of broad spectrum hydrolases. ChemBioChem 16 (2015) 2466–2469. [DOI] [PMID: 26316208]
[EC 3.1.3.104 created 2016]
 
 
EC 4.3.1.32     
Accepted name: 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase
Reaction: 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil + S-adenosyl-L-methionine = 7,8-didemethyl-8-hydroxy-5-deazariboflavin + NH3 + L-methionine + 5′-deoxyadenosine
Other name(s): FO synthase; fbiC (gene name) (ambiguous); cofG (gene name)
Systematic name: 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5,6-dihydrouracil ammonia-lyase (7,8-didemethyl-8-hydroxy-5-deazariboflavin-forming)
Comments: The enzyme produces the 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) precursor of the redox cofactor coenzyme F420, which is found in methanogens and in various actinobacteria. FO is also produced by some cyanobacteria and eukaryotes. The enzyme, which forms a complex with EC 2.5.1.147, 5-amino-6-(D-ribitylamino)uracilL-tyrosine 4-hydroxyphenyl transferase, is a radical SAM enzyme that uses the 5′-deoxyadenosyl radical to catalyse the condensation reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Decamps, L., Philmus, B., Benjdia, A., White, R., Begley, T.P. and Berteau, O. Biosynthesis of F0, precursor of the F420 cofactor, requires a unique two radical-SAM domain enzyme and tyrosine as substrate. J. Am. Chem. Soc. 134 (2012) 18173–18176. [DOI] [PMID: 23072415]
2.  Philmus, B., Decamps, L., Berteau, O. and Begley, T.P. Biosynthetic versatility and coordinated action of 5′-deoxyadenosyl radicals in deazaflavin biosynthesis. J. Am. Chem. Soc. 137 (2015) 5406–5413. [DOI] [PMID: 25781338]
[EC 4.3.1.32 created 2010 as EC 2.5.1.77, part transferred 2018 to EC 4.3.1.32]
 
 


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