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3)-β-D-galactosyl-(13)-N-acetyl-D-galactosaminyl-R = CMP + N-acetyl-α-neuraminyl-(23)-β-D-galactosyl-(13)-[N-acetyl-α-neuraminyl-(26)]-N-acetyl-D-galactosaminyl-R
An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Common name: GDP-4-dehydro-6-deoxy-D-mannose reductase
Reaction: GDP-6-deoxy-D-mannose + NAD(P)+ = GDP-4-dehydro-6-deoxy-D-mannose + NAD(P)H + H+
For diagram click here.
Other name(s): GDP-4-keto-6-deoxy-D-mannose reductase [ambiguous]; GDP-6-deoxy-D-lyxo-4-hexulose reductase; Rmd
Systematic name: GDP-6-deoxy-D-mannose:NAD(P)+ 4-oxidoreductase (D-rhamnose-forming)
Comments: This enzyme differs from EC 1.1.1.187, GDP-4-dehydro-D-rhamnose reductase, in that the only product formed is GDP-D-rhamnose (GDP-6-deoxy-D-mannose). D-Rhamnose is a constituent of lipopolysaccharides of Gram-negative plant and human pathogenic bacteria.
References:
1. Kneidinger, B., Graninger, M., Adam, G., Puchberger, M., Kosma, P., Zayni, S. and Messner, P. Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 276 (2001) 5577-5583. [PMID: 11096116]
2. Mäki, M., Järvinen, N., Räbinä, J., Roos, C., Maaheimo, H., Mattila, P. and Renkonen, R. Functional expression of Pseudomonas aeruginosa GDP-4-keto-6-deoxy-D-mannose reductase which synthesizes GDP-rhamnose. Eur. J. Biochem. 269 (2002) 593-601. [PMID: 11856318]
Common name: precorrin-6A reductase
Reaction: precorrin-6B + NADP+ = precorrin-6A + NADPH + H+
For diagram click here.
Other name(s): precorrin-6X reductase; precorrin-6Y:NADP+ oxidoreductase
Systematic name: precorrin-6B:NADP+ oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 137672-84-5
References:
1. Blanche, F., Thibaut, D., Famechon, A., Debussche, L., Cameron, B. and Crouzet, J. Precorrin-6X reductase from Pseudomonas denitrificans: purification and characterization of the enzyme and identification of the structural gene. J. Bacteriol. 174 (1992) 1036-1042. [PMID: 1732193]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: precorrin-2 dehydrogenase
Reaction: precorrin-2 + NAD+ = sirohydrochlorin + NADH + H+
For diagram click here.
Other name(s): Met8p; SirC; CysG
Systematic name: precorrin-2:NAD+ oxidoreductase
Comments: This enzyme catalyses the second of three steps leading to the formation of siroheme from uroporphyrinogen III. The first step involves the donation of two S-adenosyl-L-methionine-derived methyl groups to carbons 2 and 7 of uroporphyrinogen III to form precorrin-2 (EC 2.1.1.107, uroporphyrin-III C-methyltransferase) and the third step involves the chelation of ferrous iron to sirohydrochlorin to form siroheme (EC 4.99.1.4, sirohydrochlorin ferrochelatase). In Saccharomyces cerevisiae, the last two steps are carried out by a single bifunctional enzyme, Met8p. In some bacteria, steps 1-3 are catalysed by a single multifunctional protein called CysG, whereas in Bacillus megaterium, three separate enzymes carry out each of the steps, with SirC being responsible for the above reaction.
References:
1. Schubert, H.L., Raux, E., Brindley, A.A., Leech, H.K., Wilson, K.S., Hill, C.P. and Warren, M.J. The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase. EMBO J. 21 (2002) 2068-2075. [PMID: 11980703]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: 1,2-dehydroreticulinium reductase (NADPH)
Reaction: (R)-reticuline + NADP+ = 1,2-dehydroreticulinium + NADPH + H+
For diagram click here.
Other name(s): 1,2-dehydroreticulinium ion reductase
Systematic name: (R)-reticuline:NADP+ oxidoreductase
Comments: Reduces the 1,2-dehydroreticulinium ion to (R)-reticuline, which is a direct precursor of morphinan alkaloids in the poppy plant. The enzyme does not catalyse the reverse reaction to any significant extent under physiological conditions.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 130590-58-8
References:
1. De-Eknamkul, W. and Zenk, M.H. Purification and properties of 1,2-dehydroreticulinium reductase from Papaver somniferum seedlings. Phytochemistry 31 (1992) 813-821.
Common name: 2-hydroxy-1,4-benzoquinone reductase
Reaction: 2-hydroxy-1,4-benzoquinone + NADH + H+ = 1,2,4-trihydroxybenzene + NAD+
Other name(s): hydroxybenzoquinone reductase; 1,2,4-trihydroxybenzene:NAD oxidoreductase; NADH:2-hydroxy-1,4-benzoquinone oxidoreductase
Systematic name: 2-hydroxy-1,4-benzoquinone:NADH oxidoreductase
Comments: A flavoprotein (FMN) that differs in substrate specificity from other quinone reductases. The enzyme in Burkholderia cepacia is inducible by 2,4,5-trichlorophenoxyacetate.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number:
References:
1. Zaborina, O., Daubaras, D.L., Zago, A., Xun, L., Saido, K., Klem,T., Nikolic, D. and Chakrabarty, A.M. Novel pathway for conversion of chlorohydroxyquinol to maleylacetate in Burkholderia cepacia AC1100. J. Bacteriol. 180 (1998) 4667-4675. [PMID: 9721310]
Common name: precorrin-3B synthase
Reaction: precorrin-3A + NADH + H+ + O2 = precorrin-3B + NAD+ + H2O
For diagram click here and mechanism here.
Other name(s): precorrin-3X synthase; CobG
Systematic name: precorrin-3A,NADH:oxygen oxidoreductase (20-hydroxylating)
Comments: An iron-sulfur protein. An oxygen atom from dioxygen is incorporated into the macrocycle at C-20. In the aerobic cobalamin biosynthesis pathway, four enzymes are involved in the conversion of precorrin-3A to precorrin-6A. This enzyme carries out the first of the four steps, yielding precorrin-3B as the product. This is followed by three methylation reactions, which introduce a methyl group at C-17 (CobJ), C-11 (CobM) and C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise to precorrin-4, precorrin-5 and precorrin-6A, respectively.
References:
1. Debussche, L., Thibaut, D., Cameron, B., Crouzet, J. and Blanche, F. Biosynthesis of the corrin macrocycle of coenzyme B12 in Pseudomonas denitrificans. J. Bacteriol. 175 (1993) 7430-7440. [PMID: 8226690]
2. Scott, A.I., Roessner, C.A., Stolowich, N.J., Spencer, J.B., Min, C. and Ozaki, S.I. Biosynthesis of vitamin B12. Discovery of the enzymes for oxidative ring contraction and insertion of the fourth methyl group. FEBS Lett. 331 (1993) 105-108. [PMID: 8405386]
3. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
EC 1.16.8 With flavin as acceptor
Common name: cob(II)yrinic acid a,c-diamide reductase
Reaction: 2 cob(II)yrinic acid a,c-diamide + FMN = 2 cob(I)yrinic acid a,c-diamide + FMNH2
For diagram click here.
Systematic name: cob(II)yrinic acid-a,c-diamide:FMN oxidoreductase
Comments: This enzyme also catalyses the reduction of cob(II)yric acid, cob(II)inamide, cob(II)inamide phosphate, GDP-cob(II)inamide and cob(II)alamin although cob(II)yrinic acid a,c-diamide is thought to be the physiological substrate [1]. Also uses FAD and NADH but not NADPH.
References:
1. Blanche F., Maton, L., Debussche, L. and Thibaut, D. Purification and characterization of cob(II)yrinic acid a,c-diamide reductase from Pseudomonas denitrificans. J. Bacteriol. 174 (1992) 7452-7454. [PMID: 1429467]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: uroporphyrin-III C-methyltransferase
Reaction: S-adenosyl-L-methionine + uroporphyrin III = S-adenosyl-L-homocysteine + precorrin-1
(2) S-adenosyl-L-methionine + precorrin-1 = S-adenosyl-L-homocysteine + precorrin-2
For diagram click here.
Other name(s): uroporphyrinogen methyltransferase; uroporphyrinogen-III methyltransferase; adenosylmethionine-uroporphyrinogen III methyltransferase; S-adenosyl-L-methionine-dependent uroporphyrinogen III methylase; uroporphyrinogen-III methylase; SirA; CysG; CobA [ambiguous — see EC 2.5.1.17]; SUMT
Systematic name: S-adenosyl-L-methionine:uroporphyrin-III C-methyltransferase
Comments: This enzyme catalyses two sequential methylation reactions, the first forming precorrin-1 and the second leading to the formation of precorrin-2. It is the first of three steps leading to the formation of siroheme from uroporphyrinogen III. The second step involves an NAD+-dependent dehydrogenation to form sirohydrochlorin from precorrin-2 (EC 1.3.1.76, precorrin-2 dehydrogenase) and the third step involves the chelation of Fe2+ to sirohydrochlorin to form siroheme (EC 4.99.1.4, sirohydrochlorin ferrochelatase). In Saccharomyces cerevisiae, the last two steps are carried out by a single bifunctional enzyme, Met8p. In some bacteria, steps 1-3 are catalysed by a single multifunctional protein called CysG, whereas in Bacillus megaterium, three separate enzymes carry out each of the steps, with SirA being responsible for the above reaction. Also involved in the biosynthesis of cobalamin.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 73665-99-3
References:
1. Warren, M.J., Gonzalez, M.D., Williams, H.J., Stolowich, N.J. and Scott, A.I. Uroporphyrinogen-III methylase catalyzes the enzymatic-synthesis of sirohydrochlorin-II and sirohydrochlorin-IV by a clockwise mechanism. J. Am. Chem. Soc. 112 (1990) 5343-5345.
2. Warren, M.J., Roessner, C.A., Santander, P.J. and Scott, A.I. The Escherichia coli cysG gene encodes S-adenosylmethionine-dependent uroporphyrinogen III methylase. Biochem. J. 265 (1990) 725-729. [PMID: 2407234]
3. Schubert, H.L., Raux, E., Brindley, A.A., Leech, H.K., Wilson, K.S., Hill, C.P. and Warren, M.J. The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase. EMBO J. 21 (2002) 2068-2075. [PMID: 11980703]
Common name: cobalt-factor II C20-methyltransferase
Reaction: S-adenosyl-L-methionine + cobalt-factor II = S-adenosyl-L-homocysteine + cobalt-factor III
For diagram click here.
Other name(s): CbiL
Systematic name: S-adenosyl-L-methionine:cobalt-factor-II C20-methyltransferase
Comments: Involved in the anaerobic biosynthesis of vitamin B12.
References:
1. Spencer, P., Stolowich, N.J., Sumner, L.W. and Scott, A.I. Definition of the redox states of cobalt-precorrinoids: investigation of the substrate and redox specificity of CbiL from Salmonella typhimurium. Biochemistry 37 (1998) 14917-14927. [PMID: 9778368]
Common name: precorrin-6A synthase (deacetylating)
Reaction: S-adenosyl-L-methionine + precorrin-5 + H2O = S-adenosyl-L-homocysteine + precorrin-6A + acetate
For diagram click here and mechanism here.
Other name(s): precorrin-6X synthase (deacetylating); CobF
Systematic name: S-adenosyl-L-methionine:precorrin-5 C1-methyltransferase (deacetylating)
Comments: In the aerobic cobalamin biosythesis pathway, four enzymes are involved in the conversion of precorrin-3A to precorrin-6A. The first of the four steps is carried out by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding precorrin-3B as the product. This is followed by three methylation reactions, which introduce a methyl group at C-17 (CobJ), C-11 (CobM) and C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise to precorrin-4, precorrin-5 and precorrin-6A, respectively.
References:
1. Debussche, L., Thibaut, D., Cameron, B., Crouzet, J. and Blanche, F. Biosynthesis of the corrin macrocycle of coenzyme B12 in Pseudomonas denitrificans. J. Bacteriol. 175 (1993) 7430-7440. [PMID: 8226690]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
[EC 2.4.1.93 Transferred entry: now EC 4.2.2.18, inulin fructotransferase (DFA-III-forming). The enzyme was wrongly classified as a transferase rather than a lyase. (EC 2.4.1.93 created 1976, deleted 2004)].
[EC 2.4.1.200 Transferred entry: now EC 4.2.2.17, inulin fructotransferase (DFA-I-forming). The enzyme was wrongly classified as a transferase rather than a lyase. (EC 2.4.1.200 created 1992, deleted 2004)]
Common name: (α-N-acetylneuraminyl-2,3-β-galactosyl-1,3)-N-acetyl-galactosaminide 6-α-sialyltransferase
Reaction: CMP-N-acetylneuraminate + N-acetyl-α-neuraminyl-(23)-β-D-galactosyl-(13)-N-acetyl-D-galactosaminyl-R = CMP + N-acetyl-α-neuraminyl-(23)-β-D-galactosyl-(13)-[N-acetyl-α-neuraminyl-(26)]-N-acetyl-D-galactosaminyl-R
Other name(s): sialyltransferase; cytidine monophosphoacetylneuraminate-(α-N-acetylneuraminyl-2,3-β-galactosyl-1,3)-N-acetylgalactosaminide-α-2,6-sialyltransferase; α-N-acetylneuraminyl-2,3-β-galactosyl-1,3-N-acetyl-galactosaminide α-2,6-sialyltransferase; SIAT7; ST6GALNAC
Systematic name: CMP-N-acetylneuraminate:(α-N-acetylneuraminyl-2,3-β-D-galactosyl-1,3)-N-acetyl-D-galactosaminide α-2,6-N-acetylneuraminyl-transferase
Comments: Attaches N-acetylneuraminic acid in α-2,6-linkage to N-acetyl-galactosamine only when present in the structure of α-N-acetyl-neuraminyl-2,3-β-galactosyl-1,3-N-acetylgalactosaminyl-R, where R may be protein or p-nitrophenol. Not identical with EC 2.4.99.3 α-N-acetylgalactosaminide α-2,6-sialyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 129924-24-9
References:
1. Bergh, M.L.E., Hooghwinkel, G.J.M. and Van den Eijnden, D.H. Biosynthesis of the O-glycosidically linked oligosaccharide chains of fetuin. Indications for an α-N-acetylgalactosaminide α26 sialyltransferase with a narrow acceptor specificity in fetal calf liver. J. Biol. Chem. 258 (1983) 7430-7436. [PMID: 6190802]
Common name: cob(I)yrinic acid a,c-diamide adenosyltransferase
Reaction: (1) ATP + cob(I)yrinic acid a,c-diamide = triphosphate + adenosylcob(III)yrinic acid a,c-diamide
(2) ATP + cobinamide = triphosphate + adenosylcobinamide
For diagram click here.
Other name(s): CobA; CobO; ATP:corrinoid adenosyltransferase; cob(I)alamin adenosyltransferase; aquacob(I)alamin adenosyltransferase; aquocob(I)alamin vitamin B12s adenosyltransferase; ATP:cob(I)alamin Coβ-adenosyltransferase
Systematic name: ATP:cob(I)yrinic acid-a,c-diamide Coβ-adenosyltransferase
Comments: The corrinoid adenosylation pathway comprises three steps: (i) reduction of Co(III) to Co(II) by a one-electron transfer. This can be carried out by EC 1.16.1.3, aquacobalamin reductase or non-enzymically in the presence of dihydroflavin nucleotides [2]. (ii) Co(II) is reduced to Co(I) in a second single-electron transfer by EC 1.16.1.4, cob(II)alamin reductase and (iii) the Co(I) conducts a nucleophilic attack on the adenosyl moiety of ATP to leave the cobalt atom in a Co(III) state (EC 2.5.1.17). The enzyme responsible for the adenosylation reaction is the product of the gene cobO in the aerobic bacterium Pseudomonas denitrificans and of the gene cobA in the anaerobic bacterium Salmonella typhimurium. In P. denitrificans, the enzyme shows specificity for cobyrinic acid a,c-diamide and the corrinoids that occur later in the biosynthetic pathway whereas CobA seems to have broader specificity [3]. While CobA has a preference for ATP and Mn2+, it is able to transfer a variety of nucleosides to the cobalt, including CTP, UTP and GTP, in decreasing order of preference [4] and to use Mg2+ instead of Mn2+.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 37277-84-2
References:
1. Vitols, E., Walker, G.A. and Huennekens, F.M. Enzymatic conversion of vitamin B12s to a cobamide coenzyme, α-(5,6-dimethylbenzimidazolyl)deoxyadenosylcobamide (adenosyl-B12). J. Biol. Chem. 241 (1966) 1455-1461. [PMID: 5946606]
2. Bauer, C.B., Fonseca, M.V., Holden, H.M., Thoden, J.B., Thompson, T.B., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of ATP:corrinoid adenosyltransferase from Salmonella typhimurium in its free state, complexed with MgATP, or complexed with hydroxycobalamin and MgATP. Biochemistry 40 (2001) 361-374. [PMID: 11148030]
3. Fonseca, M.V. and Escalante-Semerena, J.C. An in vitro reducing system for the enzymic conversion of cobalamin to adenosylcobalamin. J. Biol. Chem. 276 (2001) 32101-32108. [PMID: 11408479]
4. Suh, S. and Escalante-Semerena, J.C. Purification and initial characterization of the ATP:corrinoid adenosyltransferase encoded by the cobA gene of Salmonella typhimurium. J. Bacteriol. 177 (1995) 921-925. [PMID: 7860601]
[EC 2.5.1.37 Transferred entry: now EC 4.4.1.20, leukotriene-C4 synthase. The enzyme was incorrectly classified as a transferase. (EC 2.5.1.37 created 1989, deleted 2004)]
Common name: (S)-3-amino-2-methylpropionate transaminase
Reaction: (S)-3-amino-2-methylpropanoate + 2-oxoglutarate = 2-methyl-3-oxopropanoate + L-glutamate
For diagram click here.
Other name(s): L-3-aminoisobutyrate transaminase; β-aminobutyric transaminase; L-3-aminoisobutyric aminotransferase; β-aminoisobutyrate-α-ketoglutarate transaminase
Systematic name: (S)-3-amino-2-methylpropanoate:2-oxoglutarate aminotransferase
Comments: Also acts on β-alanine and other ω-amino acids having carbon chains between 2 and 5. The two enantiomers of the 2-methyl-3-oxopropanoate formed by the enzyme interconvert by enolization, so that this enzyme, together with EC 2.6.1.40, (R)-3-amino-2-methylpropionate—pyruvate transaminase, provide a route for interconversion of the enantiomers of 3-amino-2-methylpropanoate.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 9031-95-2
References:
1. Kakimoto, Y., Kanazawa, A., Taniguchi, K. and Sano, I. β-Aminoisobutyrate-α-ketoglutarate transaminase in relation to β-aminoisobutyric aciduria. Biochim. Biophys. Acta 156 (1968) 374-380. [PMID: 5641913]
2. Tamaki, N., Sakata, S.F. and Matsuda, K. Purification, properties, and sequencing of aminoisobutyrate aminotransferases from rat liver. Methods Enzymol. 324 (2000) 376-389. [PMID: 10989446]
Common name: (R)-3-amino-2-methylpropionate—pyruvate transaminase
Reaction: (R)-3-amino-2-methylpropanoate + pyruvate = 2-methyl-3-oxopropanoate + L-alanine
For diagram click here.
Other name(s): D-3-aminoisobutyrate—pyruvate transaminase; β-aminoisobutyrate-pyruvate aminotransferase; D-3-aminoisobutyrate-pyruvate aminotransferase; D-3-aminoisobutyrate-pyruvate transaminase; (R)-3-amino-2-methylpropionate transaminase; D-β-aminoisobutyrate:pyruvate aminotransferase
Systematic name: (R)-3-amino-2-methylpropanoate:pyruvate aminotransferase
Comments: The two enantiomers of the 2-methyl-3-oxopropanoate formed by the enzyme interconvert by enolization, so that this enzyme, together with EC 2.6.1.22, (S)-3-amino-2-methylpropionate transaminase, provide a route for interconversion of the enantiomers of 3-amino-2-methylpropanoate.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 37279-00-8
References:
1. Kakimoto, Y., Taniguchi, K. and Sano, I. D-β-Aminoisobutyrate:pyruvate aminotransferase in mammalian liver and excretion of β-aminoisobutyrate by man. J. Biol. Chem. 244 (1969) 335-340. [PMID: 5773299]
2. Tamaki, N., Sakata, S.F. and Matsuda, K. Purification, properties, and sequencing of aminoisobutyrate aminotransferases from rat liver. Methods Enzymol. 324 (2000) 376-389. [PMID: 10989446]
[EC 2.6.1.61 Deleted entry: (R)-3-amino-2-methylpropionate transaminase. Enzyme is identical to EC 2.6.1.40, (R)-3-amino-2-methylpropionate—pyruvate transaminase (EC 2.6.1.61 created 1982, deleted 2004)]
Common name: fucokinase
Reaction: ATP + L-fucose = ADP + β-L-fucose 1-phosphate
For diagram click here.
Other name(s): fucokinase (phosphorylating); fucose kinase; L-fucose kinase; L-fucokinase; ATP:6-deoxy-L-galactose 1-phosphotransferase
Systematic name: ATP:L-fucose 1-phosphotransferase
Comments: Requires a divalent cation for activity, with Mg2+ and Fe2+ giving rise to the highest enzyme activity. Forms part of a salvage pathway for reutilization of L-fucose. Can also phosphorylate D-arabinose, but more slowly.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 37278-00-5
References:
1. Ishihara, H., Massaro, D.J. and Heath, E.C. The metabolism of L-fucose. 3. The enzymatic synthesis of β-L-fucose 1-phosphate. J. Biol. Chem. 243 (1968) 1103-1109. [PMID: 5646161]
2. Butler, W. and Serif, G.S. Fucokinase, its anomeric specificity and mechanism of phosphate group transfer. Biochim. Biophys. Acta 829 (1985) 238-243. [PMID: 2986701]
3. Park, S.H., Pastuszak, I., Drake, R. and Elbein, A.D. Purification to apparent homogeneity and properties of pig kidney L-fucose kinase. J. Biol. Chem. 273 (1998) 5685-5691. [PMID: 9488699]
Common name: adenosylcobinamide kinase
Reaction: RTP + adenosylcobinamide = adenosylcobinamide phosphate + RDP
where RTP is either ATP or GTP (for symbol definitions, click here)
For diagram of reaction click here.
Other name(s): CobU; adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; AdoCbi kinase/AdoCbi-phosphate guanylyltransferase
Systematic name: RTP:adenosylcobinamide phosphotransferase
Comments: In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT, CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop assembly pathway, which convert adenosylcobinamide (AdoCbi) into adenosylcobalamin (AdoCbl). CobT and CobC are involved in 5,6-dimethylbenzimidazole activation whereby 5,6-dimethylbenzimidazole is converted to its riboside, α-ribazole. The second branch of the nucleotide loop assembly pathway is the cobinamide (Cbi) activation branch where AdoCbi or adenosylcobinamide-phosphate is converted to the activated intermediate AdoCbi-GDP by Cob U. The final step in adenosylcobalamin biosynthesis is the condensation of AdoCbi-GDP with α-ribazole, which is catalysed by EC 2.7.8.26, cobalamin synthase (CobS), to yield adenosylcobalamin. CobU is a bifunctional enzyme that has both kinase (EC 2.7.1.156) and guanylyltransferase (EC 2.7.7.62) activities. However, both activities are not required at all times. The kinase activity has been proposed to function only when S. typhimurium is assimilating cobinamide whereas the guanylyltransferase activity is required for both assimilation of exogenous cobinamide and for de novo synthesis of adenosylcobalamin [4].
References:
1. O'Toole, G.A. and Escalante-Semerena, J.C. Purification and characterization of the bifunctional CobU enzyme of Salmonella typhimurium LT2. Evidence for a CobU-GMP intermediate. J. Biol. Chem. 270 (1995) 23560-23569. [PMID: 7559521]
2. Thompson, T.B., Thomas, M.G., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 Å resolution. Biochemistry 37 (1998) 7686-7695. [PMID: 9601028]
3. Thompson, T.B., Thomas, M.G., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site. Biochemistry 38 (1999) 12995-13005. [PMID: 10529169]
4. Thomas, M.G., Thompson, T.B., Rayment, I. and Escalante-Semerena, J.C. Analysis of the adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase (CobU) enzyme of Salmonella typhimurium LT2. Identification of residue His-46 as the site of guanylylation. J. Biol. Chem. 275 (2000) 27576-27586. [PMID: 10869342]
5. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: adenosylcobinamide-phosphate guanylyltransferase
Reaction: GTP + adenosylcobinamide phosphate = diphosphate + adenosylcobinamide-GDP
For diagram click here.
Other name(s): CobU; adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; GTP:adenosylcobinamide-phosphate guanylyltransferase; AdoCbi kinase/AdoCbi-phosphate guanylyltransferase
Systematic name: GTP:adenosylcobinamide-phosphate guanylyltransferase
Comments: In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT, CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop assembly pathway, which convert adenosylcobinamide (AdoCbi) into adenosylcobalamin (AdoCbl). CobT and CobC are involved in 5,6-dimethylbenzimidazole activation whereby 5,6-dimethylbenzimidazole is converted to its riboside, α-ribazole. The second branch of the nuclotide loop assembly pathway is the cobinamide (Cbi) activation branch where AdoCbi or adenosylcobinamide-phosphate is converted to the activated intermediate AdoCbi-GDP by the bifunctional enzyme Cob U. The final step in adenosylcobalamin biosynthesis is the condensation of AdoCbi-GDP with α-ribazole, which is catalysed by EC 2.7.8.26, cobalamin synthase (CobS), to yield adenosylcobalamin. CobU is a bifunctional enzyme that has both kinase (EC 2.7.1.156) and guanylyltransferase (EC 2.7.7.62) activities. However, both activities are not required at all times. The kinase activity has been proposed to function only when S. typhimurium is assimilating cobinamide whereas the guanylyltransferase activity is required for both assimilation of exogenous cobinamide and for de novo synthesis of adenosylcobalamin [4]. The guanylyltransferase reaction is a two-stage reaction with formation of a CobU-GMP intermediate [1]. Guanylylation takes place at histidine-46.
References:
1. O'Toole, G.A. and Escalante-Semerena, J.C. Purification and characterization of the bifunctional CobU enzyme of Salmonella typhimurium LT2. Evidence for a CobU-GMP intermediate. J. Biol. Chem. 270 (1995) 23560-23569. [PMID: 7559521]
2. Thompson, T.B., Thomas, M.G., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 Å resolution. Biochemistry 37 (1998) 7686-7695. [PMID: 9601028]
3. Thompson, T.B., Thomas, M.G., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site. Biochemistry 38 (1999) 12995-13005. [PMID: 10529169]
4. Thomas, M.G., Thompson, T.B., Rayment, I. and Escalante-Semerena, J.C. Analysis of the adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase (CobU) enzyme of Salmonella typhimurium LT2. Identification of residue His-46 as the site of guanylylation. J. Biol. Chem. 275 (2000) 27576-27586. [PMID: 10869342]
5. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: adenosylcobinamide-GDP ribazoletransferase
Reaction: adenosylcobinamide-GDP + α-ribazole = GMP + adenosylcobalamin
For diagram click here.
Other name(s): CobS; cobalamin synthase; cobalamin-5'-phosphate synthase
Systematic name: adenosylcobinamide-GDP:α-ribazole ribazoletransferase
Comments: In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT, CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop assembly pathway, which convert adenosylcobinamide (AdoCbi) into adenosylcobalamin (AdoCbl). CobT and CobC are involved in 5,6-dimethylbenzimidazole activation whereby 5,6-dimethylbenzimidazole is converted to its riboside, α-ribazole. The second branch of the nuclotide loop assembly pathway is the cobinamide activation branch where AdoCbi or adenosylcobinamide-phosphate is converted to the activated intermediate AdoCbi-GDP by the bifunctional enzyme Cob U. CobS catalyses the final step in adenosylcobalamin biosynthesis, which is the condensation of AdoCbi-GDP with α-ribazole to yield adenosylcobalamin.
References:
1. Maggio-Hall, L.A. and Escalante-Semerena, J.C. In vitro synthesis of the nucleotide loop of cobalamin by Salmonella typhimurium enzymes. Proc. Natl. Acad. Sci. USA 96 (1999) 11798-11803. [PMID: 10518530]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: α-ribazole phosphatase
Reaction: α-ribazole 5'-phosphate + H2O = α-ribazole + phosphate
For diagram click here.
Other name(s): CobC
Systematic name: α-ribazole-5'-phosphate phosphohydrolase
Comments: In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT, CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop assembly pathway, which convert adenosylcobinamide (AdoCbi) into adenosylcobalamin (AdoCbl). CobT and CobC are involved in 5,6-dimethylbenzimidazole activation whereby 5,6-dimethylbenzimidazole is converted to its riboside, α-ribazole. The second branch of the nuclotide loop assembly pathway is the cobinamide (Cbi) activation branch where AdoCbi or adenosylcobinamide-phosphate is converted to the activated intermediate AdoCbi-GDP by the bifunctional enzyme Cob U. CobS catalyses the final step in adenosylcobalamin biosynthesis, which is the condensation of AdoCbi-GDP with α-ribazole to yield adenosylcobalamin.
References:
1. O'Toole, G.A., Trzebiatowski, J.R. and Escalante-Semerena, J.C. The cobC gene of Salmonella typhimurium codes for a novel phosphatase involved in the assembly of the nucleotide loop of cobalamin. J. Biol. Chem. 269 (1994) 26503-26511. [PMID: 7929373]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: 2,6-β-fructan 6-levanbiohydrolase
Reaction: Hydrolysis of 2,6-β-D-fructofuranan, to remove successive disaccharide residues as levanbiose, i.e. 6-(β-D-fructofuranosyl)-D-fructose, from the end of the chain
Other name(s): β-2,6-fructan-6-levanbiohydrolase; 2,6-β-D-fructan 6-levanbiohydrolase; levanbiose-producing levanase; 2,6-β-D-fructan 6-β-D-fructofuranosylfructohydrolase
Systematic name: 2,6-β-D-fructofuranan 6-(β-D-fructosyl)-D-fructose-hydrolase
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 37288-46-3
References:
1. Avigad, G. and Zelikson, R. Cleavage of fructans to levanbiose by a specific hydrolase. Bull. Res. Counc. Isr. 11 (1963) 253-257.
2. Saito, K., Kondo, K., Kojima, I., Yokota, A. and Tomita, F. Purification and characterization of 2,6-β-D-fructan 6-levanbiohydrolase from Streptomyces exfoliatus F3-2. Appl. Environ. Microbiol. 66 (2000) 252-256. [PMID: 10618232]
3. Saito, K., Oda, Y., Tomita, F. and Yokota, A. Molecular cloning of the gene for 2,6-β-D-fructan 6-levanbiohydrolase from Streptomyces exfoliatus F3-2. FEMS Microbiol. Lett. 218 (2003) 265-270. [PMID: 12586402]
4. Song, E.K., Kim, H., Sung, H.K. and Cha, J. Cloning and characterization of a levanbiohydrolase from Microbacterium laevaniformans ATCC 15953. Gene 291 (2002) 45-55. [PMID: 12095678]
5. Kang, E.J., Lee, S.O., Lee, J.D., Lee, T.H. and Lee, T.H. Purification and characterization of a levanbiose-producing levanase from Pseudomonas sp. No. 43. Biotechnol. Appl. Biochem. 29 (1999) 263-268. [PMID: 10334957]
Common name: chitosanase
Reaction: Endohydrolysis of β-1,4-linkages between D-glucosamine residues in a partly acetylated chitosan
Systematic name: chitosan N-acetylglucosaminohydrolase
Comments: A whole spectrum of chitosanases are now known (for more details, see http://callisto.si.usherb.ca/~rbrzezin/index.html). They can hydrolyse various types of links in chitosan. The only constant property is the endohydrolysis of GlcN-GlcN links, which is common to all known chitosanases. One known chitosanase is limited to this link recognition [4], while the majority can also recognize GlcN-GlcNAc links or GlcNAc-GlcN links but not both. They also do not recognize GlcNAc-GlcNAc links in partly acetylated chitosan.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 51570-20-8
References:
1. Fenton, D.M. and Eveleigh, D.E. Purification and mode of action of a chitosanase from Penicillium islandicum. J. Gen. Microbiol. 126 (1981) 151-165.
2. Saito, J.-I., Kita, A., Higuchi, Y., Nagata, Y., Ando, A. and Miki, K. Crystal structure of chitosanase from Bacillus circulans MH-K1 at 1.6-Å resolution and its substrate recognition mechanism. J. Biol. Chem. 274 (1999) 30818-30825. [PMID: 10521473]
3. Izume, M., Nagae, S., Kawagishi, H., Mitsutomi, M. and Ohtakara, A. Action pattern of Bacillus sp. No. 7-M chitosanase on partially N-acetylated chitosan. Biosci. Biotechnol. Biochem. 56 (1992) 448-453. [PMID: 1368330]
4. Marcotte, E.M., Monzingo, A.F., Ernst, S.R., Brzezinski, R. and Robertus, J.D. X-ray structure of an anti-fungal chitosanase from Streptomyces N174. Nat. Struct. Biol. 3 (1996) 155-162. [PMID: 8564542]
Common name: hydroxyisourate hydrolase
Reaction: 5-hydroxyisourate + H2O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
For diagram click here.
Other name(s): HIUHase; 5-hydroxyisourate hydrolase
Systematic name: 5-hydroxyisourate amidohydrolase
Comments: The reaction is the first stage in the conversion of 5-hydroxyisourate into S-allantoin. This reaction will also occur spontaneously but more slowly.
References:
1. Raychaudhuri, A. and Tipton, P.A. A familiar motif in a new context: the catalytic mechanism of hydroxyisourate hydrolase. Biochemistry 42 (2003) 6848-6852.[PMID: 12779339]
2. Raychaudhuri, A. and Tipton, P.A. Cloning and expression of the gene for soybean hydroxyisourate hydrolase. Localization and implications for function and mechanism. Plant Physiol. 130 (2002) 2061-2068. [PMID: 12481089]
3. Sarma, A.D., Serfozo, P., Kahn, K. and Tipton, P.A. Identification and purification of hydroxyisourate hydrolase, a novel ureide-metabolizing enzyme. J. Biol. Chem. 274 (1999) 33863-33865. [PMID: 10567345]
Common name: threonine-phosphate decarboxylase
Reaction: L-threonine O-3-phosphate = (R)-1-aminopropan-2-yl phosphate + CO2
For diagram click here.
Other name(s): L-threonine-O-3-phosphate decarboxylase; CobD
Systematic name: L-threonine-O-3-phosphate carboxy-lyase
Comments: A pyridoxal-phosphate protein. This enzyme is unable to decarboxylate the D-isomer of threonine O-3-phosphate. The product of this reaction, (R)-1-aminopropan-2-yl phosphate, is the substrate of EC 6.3.1.10, adenosylcobinamide phosphate synthase, which converts adenosylcobyric acid into adenosylcobinamide phosphate in the anaerobic cobalamin biosynthesis pathway.
References:
1. Cheong, C.G., Bauer, C.B., Brushaber, K.R., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica. Biochemistry 41 (2002) 4798-4808. [PMID: 11939774]
2. Brushaber, K.R., O'Toole, G.A. and Escalante-Semerena, J.C. CobD, a novel enzyme with L-threonine-O-3-phosphate decarboxylase activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-phosphate, a proposed new intermediate in cobalamin biosynthesis in Salmonella typhimurium LT2. J. Biol. Chem. 273 (1998) 2684-2691. [PMID: 7559521]
3. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: acetylenecarboxylate hydratase
Reaction: 3-oxopropanoate = propynoate + H2O
Other name(s): acetylenemonocarboxylate hydratase; alkynoate hydratase; acetylenemonocarboxylate hydrase; acetylenemonocarboxylic acid hydrase; malonate-semialdehyde dehydratase
Systematic name: 3-oxopropanoate hydro-lyase
Comments: The reaction is effectively irreversible, favouring oxopropanoate (malonic semialdehyde) and its tautomers. Also acts on but-3-ynoate forming acetoacetate. The mechanism appears to involve hydration of the acetylene to 3-hydroxypropenoate, which will spontaneously tautomerize to 3-oxopropanoate. It is thus analogous to EC 4.1.1.78, acetylenedicarboxylate decarboxylase, in its mechanism.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 9024-26-4
References:
1. Van den Tweel, W.J.J. and De Bont, J.A.M. Metabolism of 3-butyn-1-ol by Pseudomonas BB1. J. Gen. Microbiol. 131 (1985) 3155-3162.
2. Yamada, E.W. and Jakoby, W.B. Enzymatic utilization of acetylenic compounds. II. Acetylenemonocarboxylic acid hydrase. J. Biol. Chem. 234 (1959) 941-945. [PMID: 13654296]
Common name: GDP-mannose 4,6-dehydratase
Reaction: GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H2O
For diagram click here.
Other name(s): guanosine 5'-diphosphate-D-mannose oxidoreductase; guanosine diphosphomannose oxidoreductase; guanosine diphosphomannose 4,6-dehydratase; GDP-D-mannose dehydratase; GDP-D-mannose 4,6-dehydratase; Gmd
Systematic name: GDP-mannose 4,6-hydro-lyase
Comments: The bacterial enzyme requires bound NAD+. This enzyme forms the first step in the biosynthesis of GDP-D-rhamnose and GDP-L-fucose. In Aneurinibacillus thermoaerophilus L420-91T, this enzyme acts as a bifunctional enzyme, catalysing the above reaction as well as the reaction catalysed by EC 1.1.1.281, GDP-4-dehydro-6-deoxy-D-mannose reductase [5]. Belongs to the short-chain dehydrogenase/reductase enzyme family, having homologous structures and a conserved catalytic triad of Lys, Tyr and Ser/Thr residues [6].
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 37211-59-9
References:
1. Elbein, A.D. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. II. Guanosine diphosphate 4-keto-6-deoxy-D-mannose, an intermediate in the biosynthesis of guanosine diphosphate colitose. J. Biol. Chem. 240 (1965) 1926-1931. [PMID: 14299611]
2. Liao, T.-H. and Barber, G.A. Purification of guanosine 5'-diphosphate D-mannose oxidoreductase from Phaseolus vulgaris. Biochim. Biophys. Acta 276 (1972) 85-93. [PMID: 5047712]
3. Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467-1474. [PMID: 4869560]
4. Sullivan, F.X., Kumar, R., Kriz, R., Stahl, M., Xu, G.Y., Rouse, J., Chang, X.J., Boodhoo, A., Potvin, B. and Cumming, D.A. Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro. J. Biol. Chem. 273 (1988) 8193-8202. [PMID: 9525924]
5. Kneidinger, B., Graninger, M., Adam, G., Puchberger, M., Kosma, P., Zayni, S. and Messner, P. Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 276 (2001) 5577-5583. [PMID: 11096116]
6. Mulichak, A.M., Bonin, C.P., Reiter, W.D. and Garavito, R.M. Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity. Biochemistry 41 (2000) 15578-15589. [PMID: 12501186]
[EC 4.2.1.71 Deleted entry: acetylenecarboxylate hydratase. This enzyme is identical to EC 4.2.1.27, acetylenecarboxylate hydratase (EC 4.2.1.71 created 1978, modified 1989, modified 2000, deleted 2004)]
Common name: levan fructotransferase (DFA-IV-forming)
Reaction: Produces di-β-D-fructofuranose 2,6':2',6-dianhydride (DFA IV) by successively eliminating the diminishing (26)-β-D-fructan
(levan) chain from the terminal D-fructosyl-D-fructosyl disaccharide.
For diagram click here.
Other name(s): 2,6-β-D-fructan D-fructosyl-D-fructosyltransferase (forming di-β-D-fructofuranose 2,6':2',6-dianhydride); levan fructotransferase
Systematic name: 2,6-β-D-fructan lyase (di-β-D-fructofuranose-2,6':2',6-dianhydride-forming)
Comments: This enzyme, like EC 4.2.2.17 [inulin fructotransferase (DFA-I-forming)] and EC 4.2.2.18 [inulin fructotransferase (DFA-III-forming)] eliminates the fructan chain from the terminal disaccharide leaving a difructose dianhydride. These enzymes have long been known as fructotransferases, so this is retained in the common name. Since the transfer is intramolecular, the reaction is an elimination and, hence, the enzyme is a lyase, belonging in EC 4.
References:
1. Song, K.B., Bae, K.S., Lee, Y.B., Lee, K.Y. and Rhee, S.K. Characteristics of levan fructotransferase from Arthrobacter ureafaciens K2032 and difructose anhydride IV formation from levan. Enzyme Microb. Technol. 27 (2000) 212-218.
2. Jang, K.H., Ryu, E.J., Park, B.S., Song, K.B., Kang, S.A., Kim, C.H., Uhm, T.B., Park, Y.I. and Rhee, S.K. Levan fructotransferase from Arthrobacter oxydans, J17-21 catalyzes the formation of the di-D-fructose dianhydride IV from levan. J. Agric. Food Chem. 51 (2003) 2632-2636. [PMID: 12696949]
3. Saito, K. and Tomita, F. Difructose anhydrides: Their mass-production and physiological functions. Biosci. Biotechnol. Biochem. 64 (2000) 1321-1327. [PMID: 10945246]
Common name: inulin fructotransferase (DFA-I-forming)
Reaction: Produces α-D-fructofuranose β-D-fructofuranose 1,2':2,1'-dianhydride (DFA I) by successively eliminating the diminishing (21)-β-D-fructan (inulin) chain from the terminal D-fructosyl-D-fructosyl disaccharide.
For diagram click here.
Other name(s): inulin fructotransferase (DFA-I-producing); inulin fructotransferase (depolymerizing, difructofuranose-1,2':2',1-dianhydride-forming); inulin D-fructosyl-D-fructosyltransferase (1,2':1',2-dianhydride-forming); inulin D-fructosyl-D-fructosyltransferase (forming α-D-fructofuranose β-D-fructofuranose 1,2':1',2-dianhydride)
Systematic name: 2,1-β-D-fructan lyase (α-D-fructofuranose-β-D-fructofuranose-1,2':2,1'-dianhydride-forming)
Comments: This enzyme, like EC 4.2.2.16 [levan fructotransferase (DFA-IV-forming)] and EC 4.2.2.18 [inulin fructotransferase (DFA-III-forming)] eliminates the fructan chain from the terminal disaccharide leaving a difructose dianhydride. These enzymes have long been known as fructotransferases, so this is retained in the common name. Since the transfer is intramolecular, the reaction is an elimination and, hence, the enzyme is a lyase, belonging in EC 4.
Links to other databases: BRENDA, EXPASY, KEGG, ERGO, CAS registry number: 125008-19-7
References:
1. Seki, K., Haraguchi, K., Kishimoto, M., Kobayashi, S. and Kainuma, K. Purification and properties of a novel inulin fructotransferase (DFA I-producing) from Arthrobacter globiformis S14-3. Agric. Biol. Chem. 53 (1989) 2089-2094.
Common name: inulin fructotransferase (DFA-III-forming)
Reaction: Produces α-D-fructofuranose β-D-fructofuranose 1,2':2,3'-dianhydride (DFA III) by successively eliminating the diminishing (21)-β-D-fructan (inulin) chain from the terminal D-fructosyl-D-fructosyl disaccharide.
For diagram click here.
Other name(s): inulin fructotransferase (DFA-III-producing); inulin fructotransferase (depolymerizing); inulase II; inulinase II; inulin fructotransferase (depolymerizing, difructofuranose-1,2':2,3'-dianhydride-forming); inulin D-fructosyl-D-fructosyltransferase (1,2':2,3'-dianhydride-forming); inulin D-fructosyl-D-fructosyltransferase (forming α-D-fructofuranose β-D-fructofuranose 1,2':2,3'-dianhydride)
Systematic name: 2,1-β-D-fructan lyase (α-D-fructofuranose-β-D-fructofuranose-1,2':2,3'-dianhydride-forming)
Comments: This enzyme, like EC 4.2.2.16 [levan fructotransferase (DFA-IV-forming)] and EC 4.2.2.17 [inulin fructotransferase (DFA-I-forming)] eliminates the fructan chain from the terminal disaccharide leaving a difructose dianhydride. These enzymes have long been known as fructotransferases, so this is retained in the common name. Since the transfer is intramolecular, the reaction is an elimination and, hence, the enzyme is a lyase, belonging in EC 4.
Links to other databases: BRENDA, EXPASY, KEGG, ERGO, CAS registry number: 50936-42-0
References:
1. Uchiyama, T. Action of Arthrobacter ureafaciens inulinase II on several oligofructans and bacterial levans. Biochim. Biophys. Acta 397 (1975) 153-163. [PMID: 1148257]
2. Uchiyama, T., Niwa, S. and Tanaka, K. Purification and properties of Arthrobacter ureafaciens inulase II. Biochim. Biophys. Acta 315 (1973) 412-420.
Common name: glucosaminate ammonia-lyase
Reaction: D-glucosaminate = 2-dehydro-3-deoxy-D-gluconate + NH3
Other name(s): glucosaminic dehydrase; D-glucosaminate dehydratase; D-glucosaminic acid dehydrase; aminodeoxygluconate dehydratase; 2-amino-2-deoxy-D-gluconate hydro-lyase (deaminating); aminodeoxygluconate ammonia-lyase; 2-amino-2-deoxy-D-gluconate ammonia-lyase
Systematic name: D-glucosaminate ammonia-lyase (isomerizing)
Comments: Contains pyridoxal phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 37290-91-8
References:
1. Imanaga, Y. Metabolism of D-glucosamine. III. Enzymic degradation of D-glucosaminic acid. J. Biochem. (Tokyo) 45 (1958) 647-650.
2. Merrick, J.M. and Roseman, S. D-Glucosaminic acid dehydrase. Methods Enzymol. 9 (1966) 657-660.
3. Iwamoto, R., Imanaga, Y. and Soda, K. D-Glucosaminate dehydratase from Agrobacterium radiobacter. Physicochemical and enzymological properties. J. Biochem. (Tokyo) 91 (1982) 283-289. [PMID: 7068563]
4. Iwamoto, R., Taniki, H., Koishi, J. and Nakura, S. D-Glucosaminate aldolase activity of D-glucosaminate dehydratase from Pseudomonas fluorescens and its requirement for Mn2+ ion. Biosci. Biotechnol. Biochem. 59 (1995) 408-411. [PMID: 7766176]
[EC 4.3.1.21 Deleted entry: aminodeoxygluconate ammonia-lyase. Enzyme is identical to EC 4.3.1.9, glucosaminate ammonia-lyase (EC 4.3.1.21 created 1965 as EC 4.2.1.26, transferred 2002 to EC 4.3.1.21, deleted 2004)]
Common name: leukotriene-C4 synthase
Reaction: leukotriene C4 = leukotriene A4 + glutathione
For diagram click here.
Other name(s): leukotriene C4 synthetase; LTC4 synthase; LTC4 synthetase; leukotriene A4:glutathione S-leukotrienyltransferase; (7E,9E,11Z,14Z)-(5S,6R)-5,6-epoxyicosa-7,9,11,14-tetraenoate:glutathione leukotriene-transferase (epoxide-ring-opening)
Systematic name: (7E,9E,11Z,14Z)-(5S,6R)-6-(glutathion-S-yl)-5-hydroxyicosa-7,9,11,14-tetraenoate glutathione-lyase (epoxide-forming)
Comments: The reaction proceeds in the direction of addition. Not identical with EC 2.5.1.18, glutathione transferase.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 90698-32-1
References:
1. Bach, M.K., Brashler, J.R. and Morton, D.R., Jr. Solubilization and characterization of the leukotriene C4 synthetase of rat basophil leukemia cells: a novel, particulate glutathione S-transferase. Arch. Biochem. Biophys. 230 (1984) 455-465. [PMID: 6324687]
2. Shimizu, T. Enzymes functional in the syntheses of leukotrienes and related compounds. Int. J. Biochem. 20 (1988) 661-666. [PMID: 2846379]
3. Lam, B.K. and Austen, K.F. Leukotriene C4 synthase: a pivotal enzyme in cellular biosynthesis of the cysteinyl leukotrienes. Prostaglandins Other Lipid Mediat. 68-69 (2002) 511-520. [PMID: 12432940]
4. Christmas, P., Weber, B.M., McKee, M., Brown, D. and Soberman, R.J. Membrane localization and topology of leukotriene C4 synthase. J. Biol. Chem. 277 (2002) 28902-28908. [PMID: 12023288]
Common name: sirohydrochlorin cobaltochelatase
Reaction: sirohydrochlorin + Co2+ = cobalt-sirohydrochlorin + 2 H+
For diagram click here.
Other name(s): CbiK; CbiX; CbiXS; anaerobic cobalt chelatase; cobaltochelatase [ambiguous]
Systematic name: sirohydrochlorin cobalt-lyase
Comments: This enzyme is a type II chelatase, being either a monomer (CbiX) or a homodimer (CibK) and being ATP-independent. CbiK from Salmonella enterica uses precorrin-2 as the substrate to yield cobalt-precorrin-2. The enzyme contains two histidines at the active site that are thought to be involved in the deprotonation of the tetrapyrrole substrate as well as in metal binding. CbiX from Bacillus megaterium inserts cobalt at the level of sirohydrochlorin (factor-II) rather than precorrin-2.
References:
1. Schubert, H.L., Raux, E., Wilson, K.S. and Warren, M.J. Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis. Biochemistry 38 (1999) 10660-10669. [PMID: 10451360]
2. Brindley, A.A., Raux E., Leech, H.K., Schubert, H.L. and Warren, M.J. A story of chelatase evolution: Identification and characterisation of a small 13-15 kDa 'ancestral' cobaltochelatase (CbiXS) in the Archaea. J. Biol. Chem. 278 (2003) 22388-22395. [PMID: 12686546]
3. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: sirohydrochlorin ferrochelatase
Reaction: sirohydrochlorin + Fe2+ = siroheme + 2 H+
For diagram click here.
Other name(s): CysG; Met8P; SirB
Systematic name: sirohydrochlorin ferro-lyase
Comments: This enzyme catalyses the third of three steps leading to the formation of siroheme from uroporphyrinogen III. The first step involves the donation of two S-adenosyl-L-methionine-derived methyl groups to carbons 2 and 7 of uroporphyrinogen III to form precorrin-2 (EC 2.1.1.107, uroporphyrin-III C-methyltransferase) and the second step involves an NAD+-dependent dehydrogenation to form sirohydrochlorin from precorrin-2 (EC 1.3.1.76, precorrin-2 dehydrogenase). In Saccharomyces cerevisiae, the last two steps are carried out by a single bifunctional enzyme, Met8p. In some bacteria, steps 1-3 are catalysed by a single multifunctional protein called CysG, whereas in Bacillus megaterium, three separate enzymes carry out each of the steps, with SirB being responsible for the above reaction.
References:
1. Schubert, H.L., Raux, E., Brindley, A.A., Leech, H.K., Wilson, K.S., Hill, C.P. and Warren, M.J. The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase. EMBO J. 21 (2002) 2068-2075. [PMID: 11980703]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: polyenoic fatty acid isomerase
Reaction: (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate = (5Z,7E,8E,14Z,17Z)-eicosapentaenoate
For diagram click here.
Other name(s): PFI; eicosapentaenoate cis-δ5,8,11,14,17-eicosapentaenoate cis-δ5-trans-δ7,9-cis-δ14,17 isomerase
Systematic name: (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate δ8,11-δ7,8-isomerase
Comments: The enzyme from the red alga Ptilota filicina catalyses the isomerization of skip dienes (methylene-interrupted double bonds) in a broad range of fatty acids and fatty-acid analogues, such as arachidonate and γ-linolenate, to yield a conjugated triene.
References:
1. Wise, M.L., Hamberg, M. and Gerwick, W.H. Biosynthesis of conjugated fatty acids by a novel isomerase from the red marine alga Ptilota filicina. Biochemistry 33 (1994) 15223-15232. [PMID: 7803384]
2. Wise, M.L., Soderstrom, K., Murray, T.F. and Gerwick, W.H. Synthesis and cannabinoid receptor binding activity of conjugated triene anandamide, a novel eicosanoid. Experientia 52 (1996) 88-92. [PMID: 8575565]
3. Wise, M.L., Rossi, J. and Gerwick, W.H. Binding site characterization of polyenoic fatty-acid isomerase from the marine alga Ptilota filicina. Biochemistry 36 (1997) 2985-2992. [PMID: 9062129]
4. Zheng, W., Wise, M.L., Wyrick, A., Metz, J.G., Yuan, L. and Gerwick, W.H.Polyenoic fatty-acid isomerase from the marine red alga Ptilota filicina: protein characterization and functional expression of the cloned cDNA. Arch. Biochem. Biophys. 401 (2002) 11-20. [PMID: 12054482]
Common name: adenosylcobinamide-phosphate synthase
Reaction: (1) ATP + adenosylcobyric acid + (R)-1-aminopropan-2-yl phosphate = ADP + phosphate + adenosylcobinamide phosphate
(2) ATP + adenosylcobyric acid + (R)-1-aminopropan-2-ol = ADP + phosphate + adenosylcobinamide
For diagram click here.
Other name(s): CbiB
Systematic name: adenosylcobyric acid:(R)-1-aminopropan-2-yl phosphate ligase (ADP-forming)
Comments: This enzyme forms part of the anaerobic cobalamin biosynthesis pathway. One of the substrates for this reaction, (R)-1-aminopropan-2-yl phosphate, is produced by CobD (EC 4.1.1.81, threonine phosphate decarboxylase).
References:
1. Cheong, C.G., Bauer, C.B., Brushaber, K.R., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica. Biochemistry 41 (2002) 4798-4808. [PMID: 11939774]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing)
Reaction: 2 ATP + hydrogenobyrinic acid + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + hydrogenobyrinic acid a,c-diamide + 2 L-glutamate
For diagram click here.
Other name(s): CobB
Systematic name: hydrogenobyrinic-acid:L-glutamine amido-ligase (AMP-forming)
Comments: This step in the aerobic biosynthesis of cobalamin generates hydrogenobyrinic acid a,c-diamide, the substrate required by EC 6.6.1.2, cobaltochelatase, which adds cobalt to the macrocycle.
References:
1. Debussche, L., Thibaut, D., Cameron, B., Crouzet, J. and Blanche, F. Purification and characterization of cobyrinic acid a,c-diamide synthase from Pseudomonas denitrificans. J. Bacteriol. 172 (1990) 6239-6244. [PMID: 2172209]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: adenosylcobyric acid synthase (glutamine-hydrolysing)
Reaction: 4 ATP + adenosylcobyrinic acid a,c-diamide + 4 L-glutamine + 4 H2O = 4 ADP + 4 phosphate + adenosylcobyric acid + 4 L-glutamate
For diagram click here.
Other name(s): CobQ; cobyric acid synthase; 5'-deoxy-5'-adenosylcobyrinic-acid-a,c-diamide:L-glutamine amido-ligase; Ado-cobyric acid synthase [glutamine hydrolyzing]
Systematic name: adenosylcobyrinic-acid-a,c-diamide:L-glutamine amido-ligase (ADP-forming)
Comments: Requires Mg2+. NH3 can act instead of glutamine. This enzyme catalyses the four-step amidation sequence from cobyrinic acid a,c-diamide to cobyric acid via the formation of cobyrinic acid triamide, tetraamide and pentaamide intermediates.
References:
1. Blanche, F., Couder, M., Debussche, L., Thibaut, D., Cameron, B. and Crouzet, J. Biosynthesis of vitamin B12: stepwise amidation of carboxyl groups b, d, e, and g of cobyrinic acid a,c-diamide is catalyzed by one enzyme in Pseudomonas denitrificans. J. Bacteriol. 173 (1991) 6046-6051. [PMID: 1917839]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]
Common name: cobaltochelatase
Reaction: ATP + hydrogenobyrinic acid a,c-diamide + Co2+ = ADP + phosphate + cob(II)yrinic acid a,c-diamide + H+
For diagram click here.
Other name(s): hydrogenobyrinic acid a,c-diamide cobaltochelatase; CobNST; CobN–CobST
Systematic name: hydrogenobyrinic-acid-a,c-diamide:cobalt cobalt-ligase (ADP-forming)
Comments: This enzyme, which forms part of the aerobic cobalamin biosynthesis pathway, is a type I chelatase, being heterotrimeric and ATP-dependent. It comprises two components, one of which corresponds to CobN and the other is composed of two polypeptides, specified by cobS and cobT in Pseudomonas denitrificans, and named CobST [1]. Hydrogenobyrinic acid is a very poor substrate. ATP can be replaced by dATP or CTP but the reaction proceeds more slowly. CobN exhibits a high affinity for hydrogenobyrinic acid a,c-diamide. The oligomeric protein CobST possesses at least one sulfhydryl group that is essential for ATP-binding. Once the Co2+ is inserted, the next step in the pathway ensures that the cobalt is ligated securely by reducing Co(II) to Co(I). This step is carried out by EC 1.16.8.1, cob(II)yrinic acid a,c-diamide reductase.
References:
1. Debussche, L., Couder, M., Thibaut, D., Cameron, B., Crouzet, J. and Blanche, F. Assay, purification, and characterization of cobaltochelatase, a unique complex enzyme catalyzing cobalt insertion in hydrogenobyrinic acid a,c-diamide during coenzyme B12 biosynthesis in Pseudomonas denitrificans. J. Bacteriol. 174 (1992) 7445-7451. [PMID: 1429466]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]