The Enzyme Database

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EC 1.1.1.7     
Accepted name: propanediol-phosphate dehydrogenase
Reaction: propane-1,2-diol 1-phosphate + NAD+ = hydroxyacetone phosphate + NADH + H+
Other name(s): PDP dehydrogenase; 1,2-propanediol-1-phosphate:NAD+ oxidoreductase; propanediol phosphate dehydrogenase
Systematic name: propane-1,2-diol-1-phosphate:NAD+ oxidoreductase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9028-15-3
References:
1.  Sellinger, O.Z. and Miller, O.N. The metabolism of acetol phosphate. II. 1,2-Propanediol-1-phosphate dehydrogenase. J. Biol. Chem. 234 (1959) 1641–1646. [PMID: 13672935]
[EC 1.1.1.7 created 1961]
 
 
EC 1.1.1.8     
Accepted name: glycerol-3-phosphate dehydrogenase (NAD+)
Reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH + H+
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): α-glycerol phosphate dehydrogenase (NAD+); α-glycerophosphate dehydrogenase (NAD+); glycerol 1-phosphate dehydrogenase; glycerol phosphate dehydrogenase (NAD+); glycerophosphate dehydrogenase (NAD+); hydroglycerophosphate dehydrogenase; L-α-glycerol phosphate dehydrogenase; L-α-glycerophosphate dehydrogenase; L-glycerol phosphate dehydrogenase; L-glycerophosphate dehydrogenase (ambiguous); NAD+-α-glycerophosphate dehydrogenase; NAD+-dependent glycerol phosphate dehydrogenase; NAD+-dependent glycerol-3-phosphate dehydrogenase; NAD+-L-glycerol-3-phosphate dehydrogenase; NAD+-linked glycerol 3-phosphate dehydrogenase; NADH-dihydroxyacetone phosphate reductase; glycerol-3-phosphate dehydrogenase (NAD+); L-glycerol-3-phosphate dehydrogenase (ambiguous)
Systematic name: sn-glycerol-3-phosphate:NAD+ 2-oxidoreductase
Comments: Also acts on propane-1,2-diol phosphate and glycerone sulfate (but with a much lower affinity).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9075-65-4
References:
1.  Baranowski, T. α-Glycerophosphate dehydrogenase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 85–96.
2.  Brosemer, R.W. and Kuhn, R.W. Comparative structural properties of honeybee and rabbit α-glycerophosphate dehydrogenases. Biochemistry 8 (1969) 2095–2105. [PMID: 4307630]
3.  O'Brien, S.J. and MacIntyre, R.J. The α-glycerophosphate cycle in Drosophila melanogaster. I. Biochemical and developmental aspects. Biochem. Genet. 7 (1972) 141–161. [PMID: 4340553]
4.  Warkentin, K.L. and Fondy, T.P. Isolation and characterization of cytoplasmic L-glycerol-3-phosphate dehydrogenase from rabbit-renal-adipose tissue and its comparison with the skeletal-muscle enzyme. Eur. J. Biochem. 36 (1973) 97–109. [DOI] [PMID: 4200180]
5.  Albertyn, J., van Tonder, A. and Prior, B.A. Purification and characterization of glycerol-3-phosphate dehydrogenase of Saccharomyces cerevisiae. FEBS Lett. 308 (1992) 130–132. [DOI] [PMID: 1499720]
6.  Koekemoer, T.C., Litthauer, D. and Oelofsen, W. Isolation and characterization of adipose tissue glycerol-3-phosphate dehydrogenase. Int. J. Biochem. Cell Biol. 27 (1995) 625–632. [DOI] [PMID: 7671141]
[EC 1.1.1.8 created 1961, modified 2005]
 
 
EC 1.1.1.94     
Accepted name: glycerol-3-phosphate dehydrogenase [NAD(P)+]
Reaction: sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): L-glycerol-3-phosphate:NAD(P) oxidoreductase; glycerol phosphate dehydrogenase (nicotinamide adenine dinucleotide (phosphate)); glycerol 3-phosphate dehydrogenase (NADP); glycerol-3-phosphate dehydrogenase [NAD(P)]
Systematic name: sn-glycerol-3-phosphate:NAD(P)+ 2-oxidoreductase
Comments: The enzyme from Escherichia coli shows specificity for the B side of NADPH.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37250-30-9
References:
1.  Kito, M. and Pizer, L.I. Purification and regulatory properties of the biosynthetic L-glycerol 3-phosphate dehydrogenase from Escherichia coli. J. Biol. Chem. 244 (1969) 3316–3323. [PMID: 4389388]
2.  Edgar, J.R. and Bell, R.M. Biosynthesis in Escherichia coli of sn-glycerol 3-phosphate, a precursor of phospholipid. J. Biol. Chem. 253 (1978) 6348–6353. [PMID: 355254]
3.  Edgar, J.R. and Bell, R.M. Biosynthesis in Escherichia coli of sn-glycerol 3-phosphate, a precursor of phospholipid. Kinetic characterization of wild type and feedback-resistant forms of the biosynthetic sn-glycerol-3-phosphate dehydrogenase. J. Biol. Chem. 253 (1978) 6354–6363. [PMID: 28326]
4.  Edgar, J.R. and Bell, R.M. Biosynthesis in Escherichia coli of sn-glycerol-3-phosphate, a precursor of phospholipid. Further kinetic characterization of wild type and feedback-resistant forms of the biosynthetic sn-glycerol-3-phosphate dehydrogenase. J. Biol. Chem. 255 (1980) 3492–3497. [PMID: 6767719]
[EC 1.1.1.94 created 1972, modified 2005]
 
 
EC 1.1.1.101     
Accepted name: acylglycerone-phosphate reductase
Reaction: 1-palmitoylglycerol 3-phosphate + NADP+ = palmitoylglycerone phosphate + NADPH + H+
Other name(s): palmitoyldihydroxyacetone-phosphate reductase; palmitoyl dihydroxyacetone phosphate reductase; palmitoyl-dihydroxyacetone-phosphate reductase; acyldihydroxyacetone phosphate reductase; palmitoyl dihydroxyacetone phosphate reductase
Systematic name: 1-palmitoylglycerol-3-phosphate:NADP+ oxidoreductase
Comments: Also acts on alkylglycerone 3-phosphate and alkylglycerol 3-phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37250-35-4
References:
1.  LaBelle, E.F., Jr. and Hajira, A.K. Enzymatic reduction of alkyl and acyl derivatives of dihydroxyacetone phosphate by reduced pyridine nucleotides. J. Biol. Chem. 247 (1972) 5825–5834. [PMID: 4403490]
[EC 1.1.1.101 created 1972, modified 1976]
 
 
EC 1.1.1.156     
Accepted name: glycerol 2-dehydrogenase (NADP+)
Reaction: glycerol + NADP+ = glycerone + NADPH + H+
Other name(s): dihydroxyacetone reductase; dihydroxyacetone (reduced nicotinamide adenine dinucleotide phosphate) reductase; dihydroxyacetone reductase (NADPH); DHA oxidoreductase; glycerol 2-dehydrogenase (NADP)
Systematic name: glycerol:NADP+ 2-oxidoreductase (glycerone-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 39342-20-6
References:
1.  Ben-Amotz, A. and Avron, M. NADP specific dihydroxyacetone reductase from Dunaliella parva. FEBS Lett. 29 (1973) 153–155. [DOI] [PMID: 4146296]
[EC 1.1.1.156 created 1976]
 
 
EC 1.1.1.261     
Accepted name: sn-glycerol-1-phosphate dehydrogenase
Reaction: sn-glycerol 1-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+
For diagram of archaetidylserine biosynthesis, click here and for diagram of archaetidylserine biosynthesis, click here
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): glycerol-1-phosphate dehydrogenase [NAD(P)+]; sn-glycerol-1-phosphate:NAD+ oxidoreductase; G-1-P dehydrogenase; Gro1PDH; AraM
Systematic name: sn-glycerol-1-phosphate:NAD(P)+ 2-oxidoreductase
Comments: This enzyme is found primarily as a Zn2+-dependent form in archaea but a Ni2+-dependent form has been found in Gram-positive bacteria [6]. The Zn2+-dependent metalloenzyme is responsible for the formation of archaea-specific sn-glycerol-1-phosphate, the first step in the biosynthesis of polar lipids in archaea. It is the enantiomer of sn-glycerol 3-phosphate, the form of glycerophosphate found in bacteria and eukaryotes. The other enzymes involved in the biosynthesis of polar lipids in archaea are EC 2.5.1.41 (phosphoglycerol geranylgeranyltransferase) and EC 2.5.1.42 (geranylgeranylglycerol-phosphate geranylgeranyltransferase), which together alkylate the hydroxy groups of glycerol 1-phosphate to give unsaturated archaetidic acid, which is acted upon by EC 2.7.7.67 (CDP-archaeol synthase) to form CDP-unsaturated archaeol. The final step in the pathway involves the addition of L-serine, with concomitant removal of CMP, leading to the production of unsaturated archaetidylserine [4]. Activity of the enzyme is stimulated by K+ [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 204594-18-3
References:
1.  Nishihara, M. and Koga, Y. sn-Glycerol-1-phosphate dehydrogenase in Methanobacterium thermoautotrophicum: key enzyme in biosynthesis of the enantiomeric glycerophosphate backbone of ether phospholipids of archaebacteria. J. Biochem. 117 (1995) 933–935. [PMID: 8586635]
2.  Nishihara, M. and Koga, Y. Purification and properties of sn-glycerol-1-phosphate dehydrogenase from Methanobacterium thermoautotrophicum: characterization of the biosynthetic enzyme for the enantiomeric glycerophosphate backbone of ether polar lipids of Archaea. J. Biochem. 122 (1997) 572–576. [PMID: 9348086]
3.  Koga, Y., Kyuragi, T., Nishihara, M. and Sone, N. Did archaeal and bacterial cells arise independently from noncellular precursors? A hypothesis stating that the advent of membrane phospholipid with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent. J. Mol. Evol. 46 (1998) 54–63. [PMID: 9419225]
4.  Morii, H., Nishihara, M. and Koga, Y. CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. J. Biol. Chem. 275 (2000) 36568–36574. [DOI] [PMID: 10960477]
5.  Han, J.S. and Ishikawa, K. Active site of Zn2+-dependent sn-glycerol-1-phosphate dehydrogenase from Aeropyrum pernix K1. Archaea 1 (2005) 311–317. [PMID: 15876564]
6.  Guldan, H., Sterner, R. and Babinger, P. Identification and characterization of a bacterial glycerol-1-phosphate dehydrogenase: Ni(2+)-dependent AraM from Bacillus subtilis. Biochemistry 47 (2008) 7376–7384. [DOI] [PMID: 18558723]
[EC 1.1.1.261 created 2000, modified 2009]
 
 
EC 1.1.1.372     
Accepted name: D/L-glyceraldehyde reductase
Reaction: (1) glycerol + NADP+ = L-glyceraldehyde + NADPH + H+
(2) glycerol + NADP+ = D-glyceraldehyde + NADPH + H+
Other name(s): gld1 (gene name); gaaD (gene name)
Systematic name: glycerol:NADP+ oxidoreductase (D/L-glyceraldehyde-forming)
Comments: The enzyme takes part in a D-galacturonate degradation pathway in the fungi Aspergillus niger and Trichoderma reesei (Hypocrea jecorina). It has equal activity with D- and L-glyceraldehyde, and can also reduce glyoxal and methylglyoxal. The reaction is only observed in the direction of glyceraldehyde reduction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Liepins, J., Kuorelahti, S., Penttila, M. and Richard, P. Enzymes for the NADPH-dependent reduction of dihydroxyacetone and D-glyceraldehyde and L-glyceraldehyde in the mould Hypocrea jecorina. FEBS J. 273 (2006) 4229–4235. [DOI] [PMID: 16930134]
2.  Martens-Uzunova, E.S. and Schaap, P.J. An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet. Biol. 45 (2008) 1449–1457. [DOI] [PMID: 18768163]
[EC 1.1.1.372 created 2014]
 
 
EC 1.1.1.408     
Accepted name: 4-phospho-D-threonate 3-dehydrogenase
Reaction: 4-phospho-D-threonate + NAD+ = glycerone phosphate + CO2 + NADH + H+ (overall reaction)
(1a) 4-phospho-D-threonate + NAD+ = 3-dehydro-4-phospho-D-erythronate + NADH + H+
(1b) 3-dehydro-4-phospho-D-erythronate = glycerone phosphate + CO2 (spontaneous)
For diagram of erythronate and threonate catabolism, click here
Glossary: D-threonate = (2S,3R)-2,3,4-trihydroxybutanoate
glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): pdxA2 (gene name) (ambiguous)
Systematic name: 4-phospho-D-threonate:NAD+ 3-oxidoreductase
Comments: The enzyme, characterized from bacteria, is involved in a pathway for D-threonate catabolism.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl. Acad. Sci. USA 113 (2016) E4161–E4169. [DOI] [PMID: 27402745]
[EC 1.1.1.408 created 2017]
 
 
EC 1.1.3.21     
Accepted name: glycerol-3-phosphate oxidase
Reaction: sn-glycerol 3-phosphate + O2 = glycerone phosphate + H2O2
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): glycerol phosphate oxidase; glycerol-1-phosphate oxidase; glycerol phosphate oxidase; L-α-glycerophosphate oxidase; α-glycerophosphate oxidase; L-α-glycerol-3-phosphate oxidase
Systematic name: sn-glycerol-3-phosphate:oxygen 2-oxidoreductase
Comments: A flavoprotein (FAD).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9046-28-0
References:
1.  Gancedo, C., Gancedo, J.M. and Sols, A. Glycerol metabolism in yeasts. Pathways of utilization and production. Eur. J. Biochem. 5 (1968) 165–172. [DOI] [PMID: 5667352]
2.  Koditschek, L.K. and Umbreit, W.W. α-Glycerophosphate oxidase in Streptococcus faecium F 24. J. Bacteriol. 93 (1969) 1063–1068. [PMID: 5788698]
[EC 1.1.3.21 created 1984]
 
 
EC 1.1.5.3     
Accepted name: glycerol-3-phosphate dehydrogenase
Reaction: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): α-glycerophosphate dehydrogenase; α-glycerophosphate dehydrogenase (acceptor); anaerobic glycerol-3-phosphate dehydrogenase; DL-glycerol 3-phosphate oxidase (misleading); FAD-dependent glycerol-3-phosphate dehydrogenase; FAD-dependent sn-glycerol-3-phosphate dehydrogenase; FAD-GPDH; FAD-linked glycerol 3-phosphate dehydrogenase; FAD-linked L-glycerol-3-phosphate dehydrogenase; flavin-linked glycerol-3-phosphate dehydrogenase; flavoprotein-linked L-glycerol 3-phosphate dehydrogenase; glycerol 3-phosphate cytochrome c reductase (misleading); glycerol phosphate dehydrogenase; glycerol phosphate dehydrogenase (acceptor); glycerol phosphate dehydrogenase (FAD); glycerol-3-phosphate CoQ reductase; glycerol-3-phosphate dehydrogenase (flavin-linked); glycerol-3-phosphate:CoQ reductase; glycerophosphate dehydrogenase; L-3-glycerophosphate-ubiquinone oxidoreductase; L-glycerol-3-phosphate dehydrogenase (ambiguous); L-glycerophosphate dehydrogenase; mGPD; mitochondrial glycerol phosphate dehydrogenase; NAD+-independent glycerol phosphate dehydrogenase; pyridine nucleotide-independent L-glycerol 3-phosphate dehydrogenase; sn-glycerol 3-phosphate oxidase (misleading); sn-glycerol-3-phosphate dehydrogenase; sn-glycerol-3-phosphate:(acceptor) 2-oxidoreductase; sn-glycerol-3-phosphate:acceptor 2-oxidoreductase
Systematic name: sn-glycerol 3-phosphate:quinone oxidoreductase
Comments: This flavin-dependent dehydrogenase is an essential membrane enzyme, functioning at the central junction of glycolysis, respiration and phospholipid biosynthesis. In bacteria, the enzyme is localized to the cytoplasmic membrane [6], while in eukaryotes it is tightly bound to the outer surface of the inner mitochondrial membrane [2]. In eukaryotes, this enzyme, together with the cytosolic enzyme EC 1.1.1.8, glycerol-3-phosphate dehydrogenase (NAD+), forms the glycerol-3-phosphate shuttle by which NADH produced in the cytosol, primarily from glycolysis, can be reoxidized to NAD+ by the mitochondrial electron-transport chain [3]. This shuttle plays a critical role in transferring reducing equivalents from cytosolic NADH into the mitochondrial matrix [7,8]. Insect flight muscle uses only CoQ10 as the physiological quinone whereas hamster and rat mitochondria use mainly CoQ9 [4]. The enzyme is activated by calcium [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9001-49-4
References:
1.  Ringler, R.L. Studies on the mitochondrial α-glycerophosphate dehydrogenase. II. Extraction and partial purification of the dehydrogenase from pig brain. J. Biol. Chem. 236 (1961) 1192–1198. [PMID: 13741763]
2.  Schryvers, A., Lohmeier, E. and Weiner, J.H. Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. J. Biol. Chem. 253 (1978) 783–788. [PMID: 340460]
3.  MacDonald, M.J. and Brown, L.J. Calcium activation of mitochondrial glycerol phosphate dehydrogenase restudied. Arch. Biochem. Biophys. 326 (1996) 79–84. [DOI] [PMID: 8579375]
4.  Rauchová, H., Fato, R., Drahota, Z. and Lenaz, G. Steady-state kinetics of reduction of coenzyme Q analogs by glycerol-3-phosphate dehydrogenase in brown adipose tissue mitochondria. Arch. Biochem. Biophys. 344 (1997) 235–241. [DOI] [PMID: 9244403]
5.  Shen, W., Wei, Y., Dauk, M., Zheng, Z. and Zou, J. Identification of a mitochondrial glycerol-3-phosphate dehydrogenase from Arabidopsis thaliana: evidence for a mitochondrial glycerol-3-phosphate shuttle in plants. FEBS Lett. 536 (2003) 92–96. [DOI] [PMID: 12586344]
6.  Walz, A.C., Demel, R.A., de Kruijff, B. and Mutzel, R. Aerobic sn-glycerol-3-phosphate dehydrogenase from Escherichia coli binds to the cytoplasmic membrane through an amphipathic α-helix. Biochem. J. 365 (2002) 471–479. [DOI] [PMID: 11955283]
7.  Ansell, R., Granath, K., Hohmann, S., Thevelein, J.M. and Adler, L. The two isoenzymes for yeast NAD+-dependent glycerol 3-phosphate dehydrogenase encoded by GPD1 and GPD2 have distinct roles in osmoadaptation and redox regulation. EMBO J. 16 (1997) 2179–2187. [DOI] [PMID: 9171333]
8.  Larsson, C., Påhlman, I.L., Ansell, R., Rigoulet, M., Adler, L. and Gustafsson, L. The importance of the glycerol 3-phosphate shuttle during aerobic growth of Saccharomyces cerevisiae. Yeast 14 (1998) 347–357. [DOI] [PMID: 9559543]
[EC 1.1.5.3 created 1961 as EC 1.1.2.1, transferred 1965 to EC 1.1.99.5, transferred 2009 to EC 1.1.5.3]
 
 
EC 1.1.99.28     
Accepted name: glucose-fructose oxidoreductase
Reaction: D-glucose + D-fructose = D-gluconolactone + D-glucitol
Systematic name: D-glucose:D-fructose oxidoreductase
Comments: D-mannose, D-xylose, D-galactose, 2-deoxy-D-glucose and L-arabinose will function as aldose substrates, but with low affinities. The ketose substrate must be in the open-chain form. The apparent affinity for fructose is low, because little of the fructose substrate is in the open-chain form. Xylulose and glycerone (dihydroxyacetone) will replace fructose, but they are poor substrates. The enzyme from Zymomonas mobilis contains tightly bound NADP+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 94949-35-6
References:
1.  Zachariou, M. and Scopes, R.K. Glucose-fructose oxidoreductase: a new enzyme isolated from Zymomonas mobilis that is responsible for sorbitol production. J. Bacteriol. 167 (1986) 863–869. [DOI] [PMID: 3745122]
2.  Hardman, M.J. and Scopes, R.K. The kinetics of glucose-fructose oxidoreductase from Zymomonas mobilis. Eur. J. Biochem. 173 (1988) 203–209. [DOI] [PMID: 3356190]
3.  Kanagasundaram, V. and Scopes, R.K. Cloning, sequence analysis and expression of the structural gene encoding glucose-fructose oxidoreductase. J. Bacteriol. 174 (1992) 1439–1447. [DOI] [PMID: 1537789]
[EC 1.1.99.28 created 1999]
 
 
EC 2.2.1.2     
Accepted name: transaldolase
Reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate
For diagram of reaction, click here, of mechanism, click here and for diagram of the later stages of the pentose-phosphate pathway, click here
Other name(s): dihydroxyacetonetransferase; dihydroxyacetone synthase (incorrect); formaldehyde transketolase (incorrect)
Systematic name: sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-46-4
References:
1.  Horecker, B.L. and Smyrniotis, P.Z. Purification and properties of yeast transaldolase. J. Biol. Chem. 212 (1955) 811–825. [PMID: 14353883]
2.  Racker, E. Transaldolase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 407–412.
3.  Tsolas, O. and Horecker, B.L. Transaldolase. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 259–280.
[EC 2.2.1.2 created 1961]
 
 
EC 2.2.1.3     
Accepted name: formaldehyde transketolase
Reaction: D-xylulose 5-phosphate + formaldehyde = D-glyceraldehyde 3-phosphate + glycerone
For diagram of reaction, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): dihydroxyacetone synthase
Systematic name: D-xylulose-5-phosphate:formaldehyde glycolaldehydetransferase
Comments: A thiamine-diphosphate protein. Not identical with EC 2.2.1.1 transketolase. Also converts hydroxypyruvate and formaldehyde into glycerone and CO2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 124566-23-0
References:
1.  Bystrykh, L.V., Sokolov, A.P. and Trotsenko, Yu.A. Separation of transketolase and dihydroxyacetone synthase from methylotrophic yeasts. Dokl. Akad. Nauk S.S.S.R. 258 (1981) 499–501. [PMID: 7249920]
2.  Kato, N., Higuchi, T., Sakazawa, C., Nishizawa, T., Tani, Y. and Yamada, H. Purification and properties of a transketolase responsible for formaldehyde fixation in a methanol-utilizing yeast, Candida boidinii (Kloeckera sp.) No. 2201. Biochim. Biophys. Acta 715 (1982) 143–150. [DOI] [PMID: 7074134]
3.  Waites, M.J. and Quayle, J.R. The interrelation between transketolase and dihydroxyacetone synthase activities in the methylotrophic yeast Candida boidinii. J. Gen. Microbiol. 124 (1981) 309–316. [DOI] [PMID: 6276498]
[EC 2.2.1.3 created 1984]
 
 
EC 2.3.1.42     
Accepted name: glycerone-phosphate O-acyltransferase
Reaction: acyl-CoA + glycerone phosphate = CoA + acylglycerone phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): dihydroxyacetone phosphate acyltransferase (ambiguous)
Systematic name: acyl-CoA:glycerone-phosphate O-acyltransferase
Comments: A membrane protein. Uses CoA derivatives of palmitate, stearate and oleate, with highest activity on palmitoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37257-19-5
References:
1.  Ballas, L.M. and Bell, R.M. Topography of glycerolipid synthetic enzymes. Synthesis of phosphatidylserine, phosphatidylinositol and glycerolipid intermediates occurs on the cytoplasmic surface of rat liver microsomal vesicles. Biochim. Biophys. Acta 665 (1981) 586–595. [DOI] [PMID: 6271231]
2.  Declercq, P.E., Haagsman, H.P., Van Veldhoven, P., Debeer, L.J., Van Golde, L.M.G. and Mannaerts, G.P. Rat liver dihydroxyacetone-phosphate acyltransferases and their contribution to glycerolipid synthesis. J. Biol. Chem. 259 (1984) 9064–9075. [PMID: 6746639]
3.  Hajra, A.K. Biosynthesis of acyl dihydroxyacetone phosphate in guinea pig liver mitochondria. J. Biol. Chem. 243 (1968) 3458–3465. [PMID: 5656381]
[EC 2.3.1.42 created 1972]
 
 
EC 2.3.1.277     
Accepted name: 2-oxo-3-(phosphooxy)propyl 3-oxoalkanoate synthase
Reaction: a medium-chain 3-oxoacyl-[acyl-carrier protein] + glycerone phosphate = 2-oxo-3-(phosphooxy)propyl 3-oxoalkanoate + a holo-[acyl-carrier protein]
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): afsA (gene name); scbA (gene name); barX (gene name)
Systematic name: 3-oxoacyl-[acyl-carrier protein]:glycerone phosphate 3-oxonacylltransferase
Comments: The enzyme catalyses the first committed step in the biosynthesis of γ-butyrolactone autoregulators that control secondary metabolism and morphological development in Streptomyces bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Horinouchi, S., Suzuki, H., Nishiyama, M. and Beppu, T. Nucleotide sequence and transcriptional analysis of the Streptomyces griseus gene (afsA) responsible for A-factor biosynthesis. J. Bacteriol. 171 (1989) 1206–1210. [PMID: 2492509]
2.  Kato, J.Y., Funa, N., Watanabe, H., Ohnishi, Y. and Horinouchi, S. Biosynthesis of γ-butyrolactone autoregulators that switch on secondary metabolism and morphological development in Streptomyces. Proc. Natl. Acad. Sci. USA 104 (2007) 2378–2383. [DOI] [PMID: 17277085]
3.  Hsiao, N.H., Soding, J., Linke, D., Lange, C., Hertweck, C., Wohlleben, W. and Takano, E. ScbA from Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize γ-butyrolactones. Microbiology 153 (2007) 1394–1404. [PMID: 17464053]
4.  Lee, Y.J., Kitani, S. and Nihira, T. Null mutation analysis of an afsA-family gene, barX, that is involved in biosynthesis of the γ-butyrolactone autoregulator in Streptomyces virginiae. Microbiology 156 (2010) 206–210. [PMID: 19778967]
[EC 2.3.1.277 created 2018]
 
 
EC 2.5.1.26     
Accepted name: alkylglycerone-phosphate synthase
Reaction: 1-acyl-glycerone 3-phosphate + a long-chain alcohol = an alkyl-glycerone 3-phosphate + a long-chain acid anion
Glossary: a long-chain alcohol = an alcohol derived from a fatty acid with an aliphatic chain of 13-22 carbons.
Other name(s): alkyldihydroxyacetonephosphate synthase; alkyldihydroxyacetone phosphate synthetase; alkyl DHAP synthetase; alkyl-DHAP; dihydroxyacetone-phosphate acyltransferase (ambiguous); DHAP-AT
Systematic name: 1-acyl-glycerone-3-phosphate:long-chain-alcohol O-3-phospho-2-oxopropanyltransferase
Comments: The ester-linked fatty acid of the substrate is cleaved and replaced by a long-chain alcohol in an ether linkage.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 64060-42-0, 102484-74-2
References:
1.  Brown, A.J. and Snyder, F. Alkyldihydroxyacetone-P synthase. Solubilization, partial purification, new assay method, and evidence for a ping-pong mechanism. J. Biol. Chem. 257 (1982) 8835–8839. [PMID: 7096336]
2.  Wykle, R.L., Piantadosi, C. and Snyder, F. The role of acyldihydroxyacetone phosphate, reduced nicotinamide adenine dinucleotide, and reduced nicotinamide adenine dinucleotide phosphate in the biosynthesis of O-alkyl glycerolipids by microsomal enzymes of Ehrlich ascites tumor. J. Biol. Chem. 247 (1972) 2944–2948. [PMID: 4401994]
[EC 2.5.1.26 created 1984]
 
 
EC 2.5.1.72     
Accepted name: quinolinate synthase
Reaction: glycerone phosphate + iminosuccinate = pyridine-2,3-dicarboxylate + 2 H2O + phosphate
For diagram of quinolinate biosynthesis, click here
Glossary: quinolinate = pyridine-2,3-dicarboxylate
glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): NadA; QS; quinolinate synthetase
Systematic name: glycerone phosphate:iminosuccinate alkyltransferase (cyclizing)
Comments: An iron-sulfur protein that requires a [4Fe-4S] cluster for activity [1]. Quinolinate synthase catalyses the second step in the de novo biosynthesis of NAD+ from aspartate in some bacteria, with EC 1.4.3.16 (L-aspartate oxidase) catalysing the first step and EC 2.4.2.19 [nicotinate-nucleotide diphosphorylase (carboxylating)] the third step. In Escherichia coli, two of the residues that are involved in the [4Fe-4S] cluster binding appear to undergo reversible disulfide-bond formation that regulates the activity of the enzyme [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ollagnier-de Choudens, S., Loiseau, L., Sanakis, Y., Barras, F. and Fontecave, M. Quinolinate synthetase, an iron-sulfur enzyme in NAD biosynthesis. FEBS Lett. 579 (2005) 3737–3743. [DOI] [PMID: 15967443]
2.  Katoh, A., Uenohara, K., Akita, M. and Hashimoto, T. Early steps in the biosynthesis of NAD in Arabidopsis start with aspartate and occur in the plastid. Plant Physiol. 141 (2006) 851–857. [DOI] [PMID: 16698895]
3.  Sakuraba, H., Tsuge, H., Yoneda, K., Katunuma, N. and Ohshima, T. Crystal structure of the NAD biosynthetic enzyme quinolinate synthase. J. Biol. Chem. 280 (2005) 26645–26648. [DOI] [PMID: 15937336]
4.  Rousset, C., Fontecave, M. and Ollagnier de Choudens, S. The [4Fe-4S] cluster of quinolinate synthase from Escherichia coli: Investigation of cluster ligands. FEBS Lett. 582 (2008) 2937–2944. [DOI] [PMID: 18674537]
5.  Saunders, A.H. and Booker, S.J. Regulation of the activity of Escherichia coli quinolinate synthase by reversible disulfide-bond formation. Biochemistry 47 (2008) 8467–8469. [DOI] [PMID: 18651751]
[EC 2.5.1.72 created 2008]
 
 
EC 2.7.1.29     
Accepted name: glycerone kinase
Reaction: ATP + glycerone = ADP + glycerone phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): dihydroxyacetone kinase; acetol kinase; acetol kinase (phosphorylating)
Systematic name: ATP:glycerone phosphotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 57657-66-6
References:
1.  Sellinger, O.Z. and Miller, O.N. Phosphorylation of acetol by homogenates of rat liver. Fed. Proc. 16 (1957) 245–246.
[EC 2.7.1.29 created 1961]
 
 
EC 2.7.1.84     
Accepted name: alkylglycerone kinase
Reaction: ATP + O-alkylglycerone = ADP + O-alkylglycerone phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): alkyldihydroxyacetone kinase (phosphorylating); alkyldihydroxyacetone kinase
Systematic name: ATP:O-alkylglycerone phosphotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 52227-80-2
References:
1.  Chae, K., Piantadosi, C. and Snyder, F. Reductase, phosphatase, and kinase activities in the metabolism of alkyldihydroxyacetone phosphate and alkyldihydroxyacetone. J. Biol. Chem. 248 (1973) 6718–6723. [PMID: 4147653]
[EC 2.7.1.84 created 1976]
 
 
EC 2.7.1.121     
Accepted name: phosphoenolpyruvate—glycerone phosphotransferase
Reaction: phosphoenolpyruvate + glycerone = pyruvate + glycerone phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Systematic name: phosphoenolpyruvate:glycerone phosphotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 91755-81-6
References:
1.  Jin, R.Z. and Lin, E.C.C. An inducible phosphoenolpyruvate: dihydroxyacetone phosphotransferase system in Escherichia coli. J. Gen. Microbiol. 130 (1984) 83–88. [DOI] [PMID: 6368745]
[EC 2.7.1.121 created 1989]
 
 
EC 4.1.2.2     
Accepted name: ketotetrose-phosphate aldolase
Reaction: erythrulose 1-phosphate = glycerone phosphate + formaldehyde
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): phosphoketotetrose aldolase; erythrulose-1-phosphate synthetase; erythrose-1-phosphate synthase; erythrulose-1-phosphate formaldehyde-lyase
Systematic name: erythrulose-1-phosphate formaldehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9024-45-7
References:
1.  Charalampous, F.C. and Mueller, G.C. Synthesis of erythrulose phosphate by a soluble enzyme from rat tissue. J. Biol. Chem. 201 (1953) 161–173. [PMID: 13044785]
[EC 4.1.2.2 created 1961]
 
 
EC 4.1.2.13     
Accepted name: fructose-bisphosphate aldolase
Reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
For diagram of the pentose phosphate pathway (later stages), click here and for mechanism, click here; for diagrams of the Calvin cycle, click here and glycolysis, click here
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): aldolase; fructose-1,6-bisphosphate triosephosphate-lyase; fructose diphosphate aldolase; diphosphofructose aldolase; fructose 1,6-diphosphate aldolase; ketose 1-phosphate aldolase; phosphofructoaldolase; zymohexase; fructoaldolase; fructose 1-phosphate aldolase; fructose 1-monophosphate aldolase; 1,6-diphosphofructose aldolase; SMALDO; D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase
Systematic name: D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming)
Comments: Also acts on (3S,4R)-ketose 1-phosphates. The yeast and bacterial enzymes are zinc proteins. The enzymes increase electron-attraction by the carbonyl group, some (Class I) forming a protonated imine with it, others (Class II), mainly of microbial origin, polarizing it with a metal ion, e.g. zinc.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9024-52-6
References:
1.  Horecker, B.L., Tsolas, O. and Lai, C.Y. Aldolases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 213–258.
2.  Alefounder, P.R., Baldwin, S.A., Perham, R.N., Short, N.J. Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli. Biochem. J. 257 (1989) 529–534. [PMID: 2649077]
[EC 4.1.2.13 created 1965, modified 1999 (EC 4.1.2.7 created 1961, incorporated 1972)]
 
 
EC 4.1.2.17     
Accepted name: L-fuculose-phosphate aldolase
Reaction: L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): L-fuculose 1-phosphate aldolase; fuculose aldolase; L-fuculose-1-phosphate lactaldehyde-lyase
Systematic name: L-fuculose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9024-54-8
References:
1.  Ghalambor, M.A. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. IV. Purification and properties of cytidine monophosphate 3-deoxy-D-manno-octulosonate synthetase. J. Biol. Chem. 241 (1966) 3216–3221. [PMID: 5330266]
2.  Dreyer, M.K. and Schulz, G.E. The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli. J. Mol. Biol. 231 (1993) 549–553. [DOI] [PMID: 8515438]
3.  Dreyer, M.K. and Schulz, G.E. Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. J. Mol. Biol. 259 (1996) 458–466. [DOI] [PMID: 8676381]
[EC 4.1.2.17 created 1965]
 
 
EC 4.1.2.19     
Accepted name: rhamnulose-1-phosphate aldolase
Reaction: L-rhamnulose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
For diagram of L-Rhamnose metabolism, click here
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): rhamnulose phosphate aldolase; L-rhamnulose 1-phosphate aldolase; L-rhamnulose-phosphate aldolase; L-rhamnulose-1-phosphate lactaldehyde-lyase
Systematic name: L-rhamnulose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9054-58-4
References:
1.  Chiu, T.-H. and Feingold, D.S. L-Rhamnulose 1-phosphate aldolase from Escherichia coli. Crystallization and properties. Biochemistry 8 (1969) 98–108. [PMID: 4975916]
2.  Sawada, H. and Takagi, Y. The metabolism of L-rhamnose in Escherichia coli. 3. L-Rhamulose-phosphate aldolase. Biochim. Biophys. Acta 92 (1964) 26–32. [PMID: 14243785]
[EC 4.1.2.19 created 1972]
 
 
EC 4.1.2.29     
Accepted name: 5-dehydro-2-deoxyphosphogluconate aldolase
Reaction: 5-dehydro-2-deoxy-D-gluconate 6-phosphate = glycerone phosphate + malonate semialdehyde
For diagram of inositol catabolism, click here
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): phospho-5-keto-2-deoxygluconate aldolase; 5-dehydro-2-deoxy-D-gluconate-6-phosphate malonate-semialdehyde-lyase
Systematic name: 5-dehydro-2-deoxy-D-gluconate-6-phosphate malonate-semialdehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 62213-25-6
References:
1.  Anderson, W.A. and Magasanik, B. The pathway of myo-inositol degradation in Aerobacter aerogenes. Conversion of 2-deoxy-5-keto-D-gluconic acid to glycolytic intermediates. J. Biol. Chem. 246 (1971) 5662–5675. [PMID: 4328832]
[EC 4.1.2.29 created 1976]
 
 
EC 4.1.2.40     
Accepted name: tagatose-bisphosphate aldolase
Reaction: D-tagatose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): D-tagatose-1,6-bisphosphate triosephosphate lyase
Systematic name: D-tagatose 1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming)
Comments: Enzyme activity is stimulated by certain divalent cations. It is involved in the tagatose 6-phosphate pathway of lactose catabolism in bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 39433-95-9
References:
1.  Anderson, R.L. and Markwell, J.P. D-Tagatose-1,6-bisphosphate aldolase (class II) from Klebsiella pneumoniae. Methods Enzymol. 90 (1982) 232–234. [DOI] [PMID: 6759854]
2.  Van Rooijen, R.J., Van Schalkwijk, S., De Vos, W.M. Molecular cloning, characterization, and nucleotide sequence of the tagatose 6-phosphate pathway gene cluster of the lactose operon of Lactococcus lactis. J. Biol. Chem. 266 (1991) 7176–7181. [PMID: 1901863]
[EC 4.1.2.40 created 1999]
 
 
EC 4.1.2.57     
Accepted name: sulfofructosephosphate aldolase
Reaction: 6-deoxy-6-sulfo-D-fructose 1-phosphate = glycerone phosphate + 2-hydroxy-3-oxopropane-1-sulfonate
For diagram of sulphoglycolysis of sulfoquinovose, click here
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
2-hydroxy-3-oxopropane-1-sulfonate = 3-sulfolactaldehyde
Other name(s): yihT (gene name)
Systematic name: 6-deoxy-6-sulfofructose-1-phosphate 2-hydroxy-3-oxopropane-1-sulfonate-lyase (glycerone-phosphate-forming)
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the degradation pathway of sulfoquinovose, the polar headgroup of sulfolipids found in the photosynthetic membranes of all higher plants, mosses, ferns, algae, and most photosynthetic bacteria, as well as the surface layer of some archaea.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Denger, K., Weiss, M., Felux, A.K., Schneider, A., Mayer, C., Spiteller, D., Huhn, T., Cook, A.M. and Schleheck, D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 507 (2014) 114–117. [DOI] [PMID: 24463506]
[EC 4.1.2.57 created 2014]
 
 
EC 4.1.99.24     
Accepted name: L-tyrosine isonitrile synthase
Reaction: L-tyrosine + D-ribulose 5-phosphate = (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoate + hydroxyacetone + formaldehyde + phosphate + H2O
Glossary: (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoate = L-tyrosine isonitrile
paerucumarin = 6,7-dihydroxy-3-isocyanochromen-2-one
rhabduscin = N-[(2S,3S,4R,5S,6R)-4,5-dihydroxy-6-{4-[(E)-2-isocyanoethenyl]phenoxy}-2-methyloxan-3-yl]acetamide
Other name(s): pvcA (gene name)
Systematic name: L-tyrosine:D-ribulose-5-phosphate lyase (isonitrile-forming)
Comments: The enzymes from the bacteria Pseudomonas aeruginosa and Xenorhabdus nematophila are involved in the biosynthesis of paerucumarin and rhabduscin, respectively. According to the proposed mechanism, the enzyme forms an imine intermediate composed of linked L-tyrosine and D-ribulose 5-phosphate, followed by loss of the phosphate group and formation of a β-keto imine and keto-enol tautomerization. This is followed by a C-C bond cleavage, the release of hydroxyacetone, and a retro aldol type reaction that releases formaldehyde and forms the final product [3]. cf. EC 4.1.99.25, L-tryptophan isonitrile synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Clarke-Pearson, M.F. and Brady, S.F. Paerucumarin, a new metabolite produced by the pvc gene cluster from Pseudomonas aeruginosa. J. Bacteriol. 190 (2008) 6927–6930. [DOI] [PMID: 18689486]
2.  Drake, E.J. and Gulick, A.M. Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin. J. Mol. Biol. 384 (2008) 193–205. [DOI] [PMID: 18824174]
3.  Chang, W.C., Sanyal, D., Huang, J.L., Ittiamornkul, K., Zhu, Q. and Liu, X. In vitro stepwise reconstitution of amino acid derived vinyl isocyanide biosynthesis: detection of an elusive intermediate. Org. Lett. 19 (2017) 1208–1211. [DOI] [PMID: 28212039]
[EC 4.1.99.24 created 2018]
 
 
EC 4.1.99.25     
Accepted name: L-tryptophan isonitrile synthase
Reaction: L-tryptophan + D-ribulose 5-phosphate = (2S)-3-(1H-indol-3-yl)-2-isocyanopropanoate + hydroxyacetone + formaldehyde + phosphate + H2O
Glossary: (2S)-3-(1H-indol-3-yl)-2-isocyanopropanoate = L-tryptophan isonitrile
hydroxyacetone = 1-hydroxypropan-2-one
Other name(s): isnA (gene name); ambI1 (gene name); well1 (gene name)
Systematic name: L-tryptophan:D-ribulose-5-phosphate lyase (isonitrile-forming)
Comments: The enzymes from cyanobacteria that belong to the Nostocales order participate in the biosynthesis of hapalindole-type alkaloids. According to the proposed mechanism, the enzyme forms an imine intermediate composed of linked L-tryptophan and D-ribulose 5-phosphate, followed by loss of the phosphate group and formation of a β-keto imine and keto-enol tautomerization. This is followed by a C-C bond cleavage, the release of hydroxyacetone, and a retro aldol type reaction that releases formaldehyde and forms the final product [3]. cf. EC 4.1.99.24, L-tyrosine isonitrile synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Brady, S.F. and Clardy, J. Cloning and heterologous expression of isocyanide biosynthetic genes from environmental DNA. Angew. Chem. Int. Ed. Engl. 44 (2005) 7063–7065. [PMID: 16206308]
2.  Brady, S.F. and Clardy, J. Systematic investigation of the Escherichia coli metabolome for the biosynthetic origin of an isocyanide carbon atom. Angew. Chem. Int. Ed. Engl. 44 (2005) 7045–7048. [PMID: 16217820]
3.  Hillwig, M.L., Zhu, Q. and Liu, X. Biosynthesis of ambiguine indole alkaloids in cyanobacterium Fischerella ambigua. ACS Chem. Biol. 9 (2014) 372–377. [DOI] [PMID: 24180436]
4.  Chang, W.C., Sanyal, D., Huang, J.L., Ittiamornkul, K., Zhu, Q. and Liu, X. In vitro stepwise reconstitution of amino acid derived vinyl isocyanide biosynthesis: detection of an elusive intermediate. Org. Lett. 19 (2017) 1208–1211. [DOI] [PMID: 28212039]
[EC 4.1.99.25 created 2018]
 
 
EC 4.2.3.3     
Accepted name: methylglyoxal synthase
Reaction: glycerone phosphate = 2-oxopropanal + phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
2-oxopropanal = methylglyoxal
Other name(s): methylglyoxal synthetase; glycerone-phosphate phospho-lyase
Systematic name: glycerone-phosphate phosphate-lyase (methylglyoxal-forming)
Comments: Does not act on D-glyceraldehyde 3-phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37279-01-9
References:
1.  Cooper, R.A. and Anderson, A. The formation and catabolism of methylglyoxal during glycolysis in Escherichia coli. FEBS Lett. 11 (1970) 273–276. [DOI] [PMID: 11945504]
2.  Hopper, D.J. and Cooper, R.A. The regulation of Escherichia coli methylglyoxal synthase; a new control site in glycolysis? FEBS Lett. 13 (1971) 213–216. [DOI] [PMID: 11945670]
3.  Ray, S. and Ray, M. Isolation of methylglyoxal synthase from goat liver. J. Biol. Chem. 256 (1981) 6230–6233. [PMID: 7240200]
[EC 4.2.3.3 created 1972 as EC 4.2.99.11, transferred 2000 to EC 4.2.3.3]
 
 
EC 4.3.3.6     
Accepted name: pyridoxal 5′-phosphate synthase (glutamine hydrolysing)
Reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5′-phosphate + L-glutamate + 3 H2O + phosphate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5′-phosphate + 4 H2O + phosphate
Other name(s): PdxST
Systematic name: D-ribose 5-phosphate,D-glyceraldehyde 3-phosphate pyridoxal 5′-phosphate-lyase
Comments: The ammonia is provided by the glutaminase subunit and channeled to the active site of the lyase subunit by a 100 Å tunnel. The enzyme can also use ribulose 5-phosphate and dihydroxyacetone phosphate. The enzyme complex is found in aerobic bacteria, archaea, fungi and plants.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Burns, K.E., Xiang, Y., Kinsland, C.L., McLafferty, F.W. and Begley, T.P. Reconstitution and biochemical characterization of a new pyridoxal-5′-phosphate biosynthetic pathway. J. Am. Chem. Soc. 127 (2005) 3682–3683. [DOI] [PMID: 15771487]
2.  Raschle, T., Amrhein, N. and Fitzpatrick, T.B. On the two components of pyridoxal 5′-phosphate synthase from Bacillus subtilis. J. Biol. Chem. 280 (2005) 32291–32300. [DOI] [PMID: 16030023]
3.  Strohmeier, M., Raschle, T., Mazurkiewicz, J., Rippe, K., Sinning, I., Fitzpatrick, T.B. and Tews, I. Structure of a bacterial pyridoxal 5′-phosphate synthase complex. Proc. Natl. Acad. Sci. USA 103 (2006) 19284–19289. [DOI] [PMID: 17159152]
4.  Raschle, T., Arigoni, D., Brunisholz, R., Rechsteiner, H., Amrhein, N. and Fitzpatrick, T.B. Reaction mechanism of pyridoxal 5′-phosphate synthase. Detection of an enzyme-bound chromophoric intermediate. J. Biol. Chem. 282 (2007) 6098–6105. [DOI] [PMID: 17189272]
5.  Hanes, J.W., Keresztes, I. and Begley, T.P. Trapping of a chromophoric intermediate in the Pdx1-catalyzed biosynthesis of pyridoxal 5′-phosphate. Angew. Chem. Int. Ed. Engl. 47 (2008) 2102–2105. [DOI] [PMID: 18260082]
6.  Hanes, J.W., Burns, K.E., Hilmey, D.G., Chatterjee, A., Dorrestein, P.C. and Begley, T.P. Mechanistic studies on pyridoxal phosphate synthase: the reaction pathway leading to a chromophoric intermediate. J. Am. Chem. Soc. 130 (2008) 3043–3052. [DOI] [PMID: 18271580]
7.  Hanes, J.W., Keresztes, I. and Begley, T.P. 13C NMR snapshots of the complex reaction coordinate of pyridoxal phosphate synthase. Nat. Chem. Biol. 4 (2008) 425–430. [DOI] [PMID: 18516049]
8.  Wallner, S., Neuwirth, M., Flicker, K., Tews, I. and Macheroux, P. Dissection of contributions from invariant amino acids to complex formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase complex from Bacillus subtilis. Biochemistry 48 (2009) 1928–1935. [DOI] [PMID: 19152323]
[EC 4.3.3.6 created 2011]
 
 
EC 4.4.1.41     
Accepted name: (2S)-3-sulfopropanediol sulfolyase
Reaction: (2S)-2,3-dihydroxypropane-1-sulfonate = hydroxyacetone + sulfite
Glossary: (2S)-2,3-dihydroxypropane-1-sulfonate = (2S)-3-sulfopropanediol
Other name(s): DHPS sulfolyase; hpsG (gene name)
Systematic name: (2S)-2,3-dihydroxypropane-1-sulfonate sulfite-lyase
Comments: The enzyme, characterized from the human gut bacterium Bilophila wadsworthia, contains a glycyl radical that is generated by a dedicated activating enzyme via chemistry involving S-adenosyl-L-methionine (AdoMet) and a [4Fe-4S] cluster.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Liu, J., Wei, Y., Lin, L., Teng, L., Yin, J., Lu, Q., Chen, J., Zheng, Y., Li, Y., Xu, R., Zhai, W., Liu, Y., Liu, Y., Cao, P., Ang, E.L., Zhao, H., Yuchi, Z. and Zhang, Y. Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate. Proc. Natl. Acad. Sci. USA 117 (2020) 15599–15608. [DOI] [PMID: 32571930]
[EC 4.4.1.41 created 2021]
 
 
EC 5.3.1.1     
Accepted name: triose-phosphate isomerase
Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): phosphotriose isomerase; triose phosphoisomerase; triose phosphate mutase; D-glyceraldehyde-3-phosphate ketol-isomerase
Systematic name: D-glyceraldehyde-3-phosphate aldose-ketose-isomerase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9023-78-3
References:
1.  Meyer-Arendt, E., Beisenherz, G. and Bücher, T. Triosephosphate isomerase. Naturwissenschaften 40 (1953) 59.
2.  Meyerhof, O. and Beck, L.V. Triosephosphate isomerase. J. Biol. Chem. 156 (1944) 109–120.
[EC 5.3.1.1 created 1961]
 
 


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