The Enzyme Database

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

*EC 1.1.3.41 alditol oxidase
EC 1.1.5.3 glycerol-3-phosphate dehydrogenase
EC 1.1.99.5 transferred
EC 1.3.5.2 dihydroorotate dehydrogenase (quinone)
EC 1.3.99.11 transferred
EC 1.14.13.106 epi-isozizaene 5-monooxygenase
EC 1.14.21.7 biflaviolin synthase
EC 2.1.3.10 malonyl-S-ACP:biotin-protein carboxyltransferase
*EC 2.3.1.39 [acyl-carrier-protein] S-malonyltransferase
EC 2.3.1.187 acetyl-S-ACP:malonate ACP transferase
*EC 2.4.1.14 sucrose-phosphate synthase
EC 2.4.1.246 mannosylfructose-phosphate synthase
*EC 3.1.3.24 sucrose-phosphate phosphatase
EC 3.1.3.79 mannosylfructose-phosphate phosphatase
*EC 3.2.1.97 endo-α-N-acetylgalactosaminidase
EC 3.2.1.110 deleted
EC 4.1.1.87 malonyl-S-ACP decarboxylase
EC 4.1.1.88 biotin-independent malonate decarboxylase
EC 4.1.1.89 biotin-dependent malonate decarboxylase
EC 4.2.3.37 epi-isozizaene synthase
EC 4.3.99.2 carboxybiotin decarboxylase
EC 6.2.1.35 ACP-SH:acetate ligase


*EC 1.1.3.41
Accepted name: alditol oxidase
Reaction: an alditol + O2 = an aldose + H2O2
Other name(s): xylitol oxidase; xylitol:oxygen oxidoreductase; AldO
Systematic name: alditol:oxygen oxidoreductase
Comments: The enzyme from Streptomyces sp. IKD472 and from Streptomyces coelicolor is a monomeric oxidase containing one molecule of FAD per molecule of protein [1,2]. While xylitol (five carbons) and sorbitol (6 carbons) are the preferred substrates, other alditols, including L-threitol (four carbons), D-arabitol (five carbons), D-galactitol (six carbons) and D-mannitol (six carbons) can also act as substrates, but more slowly [1,2]. Belongs in the vanillyl-alcohol-oxidase family of enzymes [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 177322-52-0
References:
1.  Yamashita, M., Omura, H., Okamoto, E., Furuya, Y., Yabuuchi, M., Fukahi, K. and Murooka, Y. Isolation, characterization, and molecular cloning of a thermostable xylitol oxidase from Streptomyces sp. IKD472. J. Biosci. Bioeng. 89 (2000) 350–360. [PMID: 16232758]
2.  Heuts, D.P., van Hellemond, E.W., Janssen, D.B. and Fraaije, M.W. Discovery, characterization, and kinetic analysis of an alditol oxidase from Streptomyces coelicolor. J. Biol. Chem. 282 (2007) 20283–20291. [PMID: 17517896]
3.  Forneris, F., Heuts, D.P., Delvecchio, M., Rovida, S., Fraaije, M.W. and Mattevi, A. Structural analysis of the catalytic mechanism and stereoselectivity in Streptomyces coelicolor alditol oxidase. Biochemistry 47 (2008) 978–985. [PMID: 18154360]
[EC 1.1.3.41 created 2002, modified 2008]
 
 
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, IUBMB, KEGG, 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. [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. [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. [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. [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. [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. [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 1.1.99.5
Transferred entry: glycerol-3-phosphate dehydrogenase. As the acceptor is now known, the enzyme has been transferred to EC 1.1.5.3, glycerol-3-phosphate dehydrogenase.
[EC 1.1.99.5 created 1961 as EC 1.1.2.1, transferred 1965 to EC 1.1.99.5, deleted 2009]
 
 
EC 1.3.5.2
Accepted name: dihydroorotate dehydrogenase (quinone)
Reaction: (S)-dihydroorotate + a quinone = orotate + a quinol
Other name(s): dihydroorotate:ubiquinone oxidoreductase; (S)-dihydroorotate:(acceptor) oxidoreductase; (S)-dihydroorotate:acceptor oxidoreductase; DHOdehase (ambiguous); DHOD (ambiguous); DHODase (ambiguous); DHODH
Systematic name: (S)-dihydroorotate:quinone oxidoreductase
Comments: This Class 2 dihydroorotate dehydrogenase enzyme contains FMN [4]. The enzyme is found in eukaryotes in the mitochondrial membrane, in cyanobacteria, and in some Gram-negative and Gram-positive bacteria associated with the cytoplasmic membrane [2,5,6]. The reaction is the only redox reaction in the de-novo biosynthesis of pyrimidine nucleotides [2,4]. The best quinone electron acceptors for the enzyme from bovine liver are ubiquinone-6 and ubiquinone-7, although simple quinones, such as benzoquinone, can also act as acceptor at lower rates [2]. Methyl-, ethyl-, tert-butyl and benzyl (S)-dihydroorotates are also substrates, but methyl esters of (S)-1-methyl and (S)-3-methyl and (S)-1,3-dimethyldihydroorotates are not [2]. Class 1 dihydroorotate dehydrogenases use either fumarate (EC 1.3.98.1), NAD+ (EC 1.3.1.14) or NADP+ (EC 1.3.1.15) as electron acceptor.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 59088-23-2
References:
1.  Forman, H.J. and Kennedy, J. Mammalian dihydroorotate dehydrogenase: physical and catalytic properties of the primary enzyme. Arch. Biochem. Biophys. 191 (1978) 23–31. [PMID: 216313]
2.  Hines, V., Keys, L.D., III and Johnston, M. Purification and properties of the bovine liver mitochondrial dihydroorotate dehydrogenase. J. Biol. Chem. 261 (1986) 11386–11392. [PMID: 3733756]
3.  Bader, B., Knecht, W., Fries, M. and Löffler, M. Expression, purification, and characterization of histidine-tagged rat and human flavoenzyme dihydroorotate dehydrogenase. Protein Expr. Purif. 13 (1998) 414–422. [PMID: 9693067]
4.  Fagan, R.L., Nelson, M.N., Pagano, P.M. and Palfey, B.A. Mechanism of flavin reduction in Class 2 dihydroorotate dehydrogenases. Biochemistry 45 (2006) 14926–14932. [PMID: 17154530]
5.  Björnberg, O., Grüner, A.C., Roepstorff, P. and Jensen, K.F. The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. Biochemistry 38 (1999) 2899–2908. [PMID: 10074342]
6.  Nara, T., Hshimoto, T. and Aoki, T. Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene 257 (2000) 209–222. [PMID: 11080587]
[EC 1.3.5.2 created 1983 as EC 1.3.99.11, transferred 2009 to EC 1.3.5.2, modified 2011]
 
 
EC 1.3.99.11
Transferred entry: dihydroorotate dehydrogenase. As the acceptor is now known, the enzyme has been transferred to EC 1.3.5.2, dihydroorotate dehydrogenase
[EC 1.3.99.11 created 1983, deleted 2009]
 
 
EC 1.14.13.106
Accepted name: epi-isozizaene 5-monooxygenase
Reaction: (+)-epi-isozizaene + 2 NADPH + 2 H+ + 2 O2 = albaflavenone + 2 NADP+ + 3 H2O (overall reaction)
(1a) (+)-epi-isozizaene + NADPH + H+ + O2 = (5S)-albaflavenol + NADP+ + H2O
(1b) (5S)-albaflavenol + NADPH + H+ + O2 = albaflavenone + NADP+ + 2 H2O
(2a) (+)-epi-isozizaene + NADPH + H+ + O2 = (5R)-albaflavenol + NADP+ + H2O
(2b) (5R)-albaflavenol + NADPH + H+ + O2 = albaflavenone + NADP+ + 2 H2O
For diagram of reaction, click here
Glossary: epi-isozizaene
Other name(s): CYP170A1
Systematic name: (+)-epi-isozizaene,NADPH:oxygen oxidoreductase (5-hydroxylating)
Comments: This cytochrome-P-450 enzyme, from the soil-dwelling bacterium Streptomyces coelicolor A3(2), catalyses two sequential allylic oxidation reactions. The substrate epi-isozizaene, which is formed by the action of EC 4.2.3.37, epi-isozizaene synthase, is first oxidized to yield the epimeric intermediates (5R)-albaflavenol and (5S)-albaflavenol, which can be further oxidized to yield the sesquiterpenoid antibiotic albaflavenone.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 1207718-51-1
References:
1.  Zhao, B., Lin, X., Lei, L., Lamb, D.C., Kelly, S.L., Waterman, M.R. and Cane, D.E. Biosynthesis of the sesquiterpene antibiotic albaflavenone in Streptomyces coelicolor A3(2). J. Biol. Chem. 283 (2008) 8183–8189. [PMID: 18234666]
[EC 1.14.13.106 created 2008]
 
 
EC 1.14.21.7
Accepted name: biflaviolin synthase
Reaction: (1) 2 flaviolin + NADPH + H+ + O2 = 3,3′-biflaviolin + NADP+ + 2 H2O
(2) 2 flaviolin + NADPH + H+ + O2 = 3,8′-biflaviolin + NADP+ + 2 H2O
For diagram of flaviolin metabolism, click here
Glossary: flaviolin = 4,5,7-trihydroxynaphthalene-1,2-dione
3,3′-biflaviolin = 3,3′,6,6′,8,8′-hexahydroxy-2,2′-binaphthalene-1,1′,4,4′-tetraone
3,8′-biflaviolin = 2,3′,4,6′,7,8′-hexahydroxy-1,2′-binaphthalene-1′,4′,5,8-tetraone
Other name(s): CYP158A2; CYP 158A2; cytochrome P450 158A2
Systematic name: flaviolin,NADPH:oxygen oxidoreductase
Comments: This cytochrome-P-450 enzyme, from the soil-dwelling bacterium Streptomyces coelicolor A3(2), catalyses a phenol oxidation C-C coupling reaction, which results in the polymerization of flaviolin to form biflaviolin or triflaviolin without the incorporation of oxygen into the product [1,3]. The products are highly conjugated pigments that protect the bacterium from the deleterious effects of UV irradiation [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zhao, B., Guengerich, F.P., Bellamine, A., Lamb, D.C., Izumikawa, M., Lei, L., Podust, L.M., Sundaramoorthy, M., Kalaitzis, J.A., Reddy, L.M., Kelly, S.L., Moore, B.S., Stec, D., Voehler, M., Falck, J.R., Shimada, T. and Waterman, M.R. Binding of two flaviolin substrate molecules, oxidative coupling, and crystal structure of Streptomyces coelicolor A3(2) cytochrome P450 158A2. J. Biol. Chem. 280 (2005) 11599–11607. [PMID: 15659395]
2.  Zhao, B., Guengerich, F.P., Voehler, M. and Waterman, M.R. Role of active site water molecules and substrate hydroxyl groups in oxygen activation by cytochrome P450 158A2: a new mechanism of proton transfer. J. Biol. Chem. 280 (2005) 42188–42197. [PMID: 16239228]
3.  Zhao, B., Lamb, D.C., Lei, L., Kelly, S.L., Yuan, H., Hachey, D.L. and Waterman, M.R. Different binding modes of two flaviolin substrate molecules in cytochrome P450 158A1 (CYP158A1) compared to CYP158A2. Biochemistry 46 (2007) 8725–8733. [PMID: 17614370]
[EC 1.14.21.7 created 2008]
 
 
EC 2.1.3.10
Accepted name: malonyl-S-ACP:biotin-protein carboxyltransferase
Reaction: a malonyl-[acyl-carrier protein] + a biotinyl-[protein] = an acetyl-[acyl-carrier protein] + a carboxybiotinyl-[protein]
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): malonyl-S-acyl-carrier protein:biotin-protein carboxyltransferase; MadC/MadD; MadC,D; malonyl-[acyl-carrier protein]:biotinyl-[protein] carboxyltransferase
Systematic name: malonyl-[acyl-carrier protein]:biotinyl-[protein] carboxytransferase
Comments: Derived from the components MadC and MadD of the anaerobic bacterium Malonomonas rubra, this enzyme is a component of EC 4.1.1.89, biotin-dependent malonate decarboxylase. The carboxy group is transferred from malonate to the prosthetic group of the biotin protein (MadF) with retention of configuration [2]. Similar to EC 4.1.1.87, malonyl-S-ACP decarboxylase, which forms part of the biotin-independent malonate decarboxylase (EC 4.1.1.88), this enzyme also follows on from EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase, and results in the regeneration of the acetyl-[acyl-carrier protein] [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [PMID: 9128730]
2.  Micklefield, J., Harris, K.J., Gröger, S., Mocek, U., Hilbi, H., Dimroth, P. and Floss, H.G. Stereochemical course of malonate decarboxylase in Malonomonas rubra has biotin decarboxylation with retention. J. Am. Chem. Soc. 117 (1995) 1153–1154.
3.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 2.1.3.10 created 2008]
 
 
*EC 2.3.1.39
Accepted name: [acyl-carrier-protein] S-malonyltransferase
Reaction: malonyl-CoA + an [acyl-carrier protein] = CoA + a malonyl-[acyl-carrier protein]
For diagram of malonate decarboxylase, click here
Other name(s): [acyl carrier protein]malonyltransferase; FabD; malonyl coenzyme A-acyl carrier protein transacylase; malonyl transacylase; malonyl transferase; malonyl-CoA-acyl carrier protein transacylase; malonyl-CoA:[acyl-carrier-protein] S-malonyltransferase; malonyl-CoA:ACP transacylase; malonyl-CoA:ACP-SH transacylase; malonyl-CoA:AcpM transacylase; malonyl-CoA:acyl carrier protein transacylase; malonyl-CoA:acyl-carrier-protein transacylase; malonyl-CoA/dephospho-CoA acyltransferase; MAT; MCAT; MdcH
Systematic name: malonyl-CoA:[acyl-carrier protein] S-malonyltransferase
Comments: This enzyme, along with EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, is essential for the initiation of fatty-acid biosynthesis in bacteria. This enzyme also provides the malonyl groups for polyketide biosynthesis [7]. The product of the reaction, malonyl-ACP, is an elongation substrate in fatty-acid biosynthesis. In Mycobacterium tuberculosis, holo-ACP (the product of EC 2.7.8.7, holo-[acyl-carrier-protein] synthase) is the preferred substrate [5]. This enzyme also forms part of the multienzyme complexes EC 4.1.1.88 (biotin-independent malonate decarboxylase) and EC 4.1.1.89 (biotin-dependent malonate decarboxylase). Malonylation of ACP is immediately followed by decarboxylation within the malonate-decarboxylase complex to yield acetyl-ACP, the catalytically active species of the decarboxylase [12]. In the enzyme from Klebsiella pneumoniae, methylmalonyl-CoA can also act as a substrate but acetyl-CoA cannot [10] whereas the enzyme from Pseudomonas putida can use both as substrates [11]. The ACP subunit found in fatty-acid biosynthesis contains a pantetheine-4′-phosphate prosthetic group; that from malonate decarboxylase also contains pantetheine-4′-phosphate but in the form of a 2′-(5-triphosphoribosyl)-3′-dephospho-CoA prosthetic group.
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, CAS registry number: 37257-17-3
References:
1.  Alberts, A.W., Majerus, P.W. and Vagelos, P.R. Acetyl-CoA acyl carrier protein transacylase. Methods Enzymol. 14 (1969) 50–53.
2.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [PMID: 4561013]
3.  Williamson, I.P. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XVII. Preparation and general properties of acetyl coenzyme A and malonyl coenzyme A-acyl carrier protein transacylases. J. Biol. Chem. 241 (1966) 2326–2332. [PMID: 5330116]
4.  Joshi, V.C. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XXVI. Purification and properties of malonyl-coenzyme A--acyl carrier protein transacylase of Escherichia coli. Arch. Biochem. Biophys. 143 (1971) 493–505. [PMID: 4934182]
5.  Kremer, L., Nampoothiri, K.M., Lesjean, S., Dover, L.G., Graham, S., Betts, J., Brennan, P.J., Minnikin, D.E., Locht, C. and Besra, G.S. Biochemical characterization of acyl carrier protein (AcpM) and malonyl-CoA:AcpM transacylase (mtFabD), two major components of Mycobacterium tuberculosis fatty acid synthase II. J. Biol. Chem. 276 (2001) 27967–27974. [PMID: 11373295]
6.  Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S.C., Miercke, L.J., O'Connell, J.D., 3rd, Khosla, C. and Stroud, R.M. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure 11 (2003) 147–154. [PMID: 12575934]
7.  Szafranska, A.E., Hitchman, T.S., Cox, R.J., Crosby, J. and Simpson, T.J. Kinetic and mechanistic analysis of the malonyl CoA:ACP transacylase from Streptomyces coelicolor indicates a single catalytically competent serine nucleophile at the active site. Biochemistry 41 (2002) 1421–1427. [PMID: 11814333]
8.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [PMID: 9208947]
9.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [PMID: 10561613]
10.  Hoenke, S. and Dimroth, P. Formation of catalytically active acetyl-S-malonate decarboxylase requires malonyl-coenzyme A:acyl carrier protein transacylase as auxiliary enzyme. Eur. J. Biochem. 259 (1999) 181–187. [PMID: 9914491]
11.  Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37–43. [PMID: 9851033]
12.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 2.3.1.39 created 1972, modified 2006, modified 2008]
 
 
EC 2.3.1.187
Accepted name: acetyl-S-ACP:malonate ACP transferase
Reaction: an acetyl-[acyl-carrier protein] + malonate = a malonyl-[acyl-carrier protein] + acetate
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): acetyl-S-ACP:malonate ACP-SH transferase; acetyl-S-acyl-carrier protein:malonate acyl-carrier-protein-transferase; MdcA; MadA; ACP transferase; malonate/acetyl-CoA transferase; malonate:ACP transferase; acetyl-S-acyl carrier protein:malonate acyl carrier protein-SH transferase
Systematic name: acetyl-[acyl-carrier-protein]:malonate S-[acyl-carrier-protein]transferase
Comments: This is the first step in the catalysis of malonate decarboxylation and involves the exchange of an acetyl thioester residue bound to the activated acyl-carrier protein (ACP) subunit of the malonate decarboxylase complex for a malonyl thioester residue [2]. This enzyme forms the α subunit of the multienzyme complexes biotin-independent malonate decarboxylase (EC 4.1.1.88) and biotin-dependent malonate decarboxylase (EC 4.1.1.89). The enzyme can also use acetyl-CoA as a substrate but more slowly [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hilbi, H. and Dimroth, P. Purification and characterization of a cytoplasmic enzyme component of the Na+-activated malonate decarboxylase system of Malonomonas rubra: acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase. Arch. Microbiol. 162 (1994) 48–56. [PMID: 18251085]
2.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [PMID: 9208947]
3.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [PMID: 10561613]
4.  Chohnan, S., Akagi, K. and Takamura, Y. Functions of malonate decarboxylase subunits from Pseudomonas putida. Biosci. Biotechnol. Biochem. 67 (2003) 214–217. [PMID: 12619701]
5.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 2.3.1.187 created 2008]
 
 
*EC 2.4.1.14
Accepted name: sucrose-phosphate synthase
Reaction: UDP-glucose + D-fructose 6-phosphate = UDP + sucrose 6F-phosphate
Other name(s): UDP-glucose—fructose-phosphate glucosyltransferase; sucrosephosphate—UDP glucosyltransferase; UDP-glucose-fructose-phosphate glucosyltransferase; SPS; uridine diphosphoglucose-fructose phosphate glucosyltransferase; sucrose 6-phosphate synthase; sucrose phosphate synthetase; sucrose phosphate-uridine diphosphate glucosyltransferase; sucrose phosphate synthase
Systematic name: UDP-glucose:D-fructose-6-phosphate 2-α-D-glucosyltransferase
Comments: Requires Mg2+ or Mn2+ for maximal activity [2]. The enzyme from Synechocystis sp. strain PCC 6803 is not specific for UDP-glucose as it can use ADP-glucose and, to a lesser extent, GDP-glucose as substrates [2]. The enzyme from rice leaves is activated by glucose 6-phosphate but that from cyanobacterial species is not [2]. While the reaction catalysed by this enzyme is reversible, the enzyme usually works in concert with EC 3.1.3.24, sucrose-phosphate phosphatase, to form sucrose, making the above reaction essentially irreversible [3]. The F in sucrose 6F-phosphate is used to indicate that the fructose residue of sucrose carries the substituent.
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, CAS registry number: 9030-06-2
References:
1.  Mendicino, J. Sucrose phosphate synthesis in wheat germ and green leaves. J. Biol. Chem. 235 (1960) 3347–3352. [PMID: 13769376]
2.  Curatti, L., Folco, E., Desplats, P., Abratti, G., Limones, V., Herrera-Estrella, L. and Salerno, G. Sucrose-phosphate synthase from Synechocystis sp. strain PCC 6803: identification of the spsA gene and characterization of the enzyme expressed in Escherichia coli. J. Bacteriol. 180 (1998) 6776–6779. [PMID: 9852031]
3.  Huber, S.C. and Huber, J.L. Role and regulation of sucrose-phosphate synthase in higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47 (1996) 431–444. [PMID: 15012296]
4.  Cumino, A., Curatti, L., Giarrocco, L. and Salerno, G.L. Sucrose metabolism: Anabaena sucrose-phosphate synthase and sucrose-phosphate phosphatase define minimal functional domains shuffled during evolution. FEBS Lett. 517 (2002) 19–23. [PMID: 12062401]
5.  Chua, T.K., Bujnicki, J.M., Tan, T.C., Huynh, F., Patel, B.K. and Sivaraman, J. The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode. Plant Cell 20 (2008) 1059–1072. [PMID: 18424616]
[EC 2.4.1.14 created 1961, modified 2008]
 
 
EC 2.4.1.246
Accepted name: mannosylfructose-phosphate synthase
Reaction: GDP-mannose + D-fructose 6-phosphate = GDP + β-D-fructofuranosyl-α-D-mannopyranoside 6F-phosphate
Glossary: mannosylfructose = β-D-fructofuranosyl-α-D-mannopyranoside
Other name(s): mannosylfructose-6-phosphate synthase; MFPS
Systematic name: GDP-mannose:D-fructose-6-phosphate 2-α-D-mannosyltransferase
Comments: This enzyme, from the soil proteobacterium and plant pathogen Agrobacterium tumefaciens strain C58, requires Mg2+ or Mn2+ for activity. GDP-mannose can be replaced by ADP-mannose but with a concomitant decrease in activity. The product of this reaction is dephosphorylated by EC 3.1.3.79 (mannosylfructose-phosphate phosphatase) to form the non-reducing disaccharide mannosylfructose, which is the major endogenous osmolyte produced by several α-proteobacteria in response to osmotic stress. The F in the product name is used to indicate that the fructose residue of sucrose carries the substituent.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 92480-04-1 (not distinguished from EC 2.4.1.167)
References:
1.  Torres, L.L. and Salerno, G.L. A metabolic pathway leading to mannosylfructose biosynthesis in Agrobacterium tumefaciens uncovers a family of mannosyltransferases. Proc. Natl. Acad. Sci. USA 104 (2007) 14318–14323. [PMID: 17728402]
[EC 2.4.1.246 created 2008]
 
 
*EC 3.1.3.24
Accepted name: sucrose-phosphate phosphatase
Reaction: sucrose 6F-phosphate + H2O = sucrose + phosphate
Other name(s): sucrose 6-phosphate hydrolase; sucrose-phosphate hydrolase; sucrose-phosphate phosphohydrolase; sucrose-6-phosphatase; sucrose phosphatase; sucrose-6-phosphate phosphatase; SPP
Systematic name: sucrose-6F-phosphate phosphohydrolase
Comments: Requires Mg2+ for maximal activity [2]. This is the final step in the sucrose-biosynthesis pathway. The enzyme is highly specific for sucrose 6-phosphate, with fructose 6-phosphate unable to act as a substrate [2]. Belongs in the haloacid dehydrogenase (HAD) superfamily. The F of sucrose 6F-phosphate is used to indicate that the fructose residue of sucrose carries the substituent.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 9059-33-0
References:
1.  Hawker, J.S. and Hatch, M.D. A specific sucrose phosphatase from plant tissues. Biochem. J. 99 (1966) 102–107. [PMID: 4290548]
2.  Lunn, J.E., Ashton, A.R., Hatch, M.D. and Heldt, H.W. Purification, molecular cloning, and sequence analysis of sucrose-6F-phosphate phosphohydrolase from plants. Proc. Natl. Acad. Sci. USA 97 (2000) 12914–12919. [PMID: 11050182]
3.  Lunn, J.E. and MacRae, E. New complexities in the synthesis of sucrose. Curr. Opin. Plant Biol. 6 (2003) 208–214. [PMID: 12753969]
4.  Fieulaine, S., Lunn, J.E., Borel, F. and Ferrer, J.L. The structure of a cyanobacterial sucrose-phosphatase reveals the sugar tongs that release free sucrose in the cell. Plant Cell 17 (2005) 2049–2058. [PMID: 15937230]
[EC 3.1.3.24 created 1972, modified 2008]
 
 
EC 3.1.3.79
Accepted name: mannosylfructose-phosphate phosphatase
Reaction: β-D-fructofuranosyl-α-D-mannopyranoside 6F-phosphate + H2O = β-D-fructofuranosyl-α-D-mannopyranoside + phosphate
Glossary: mannosylfructose = β-D-fructofuranosyl-α-D-mannopyranoside
Other name(s): mannosylfructose-6-phosphate phosphatase; MFPP
Systematic name: β-D-fructofuranosyl-α-D-mannopyranoside-6F-phosphate phosphohydrolase
Comments: This enzyme, from the soil proteobacterium and plant pathogen Agrobacterium tumefaciens strain C58, requires Mg2+ for activity. Mannosylfructose is the major endogenous osmolyte produced by several α-proteobacteria in response to osmotic stress and is synthesized by the sequential action of EC 2.4.1.246 (mannosylfructose-phosphate synthase) followed by this enzyme. While mannosylfructose 6-phosphate is the physiological substrate, the enzyme can use sucrose 6-phosphate very efficiently. The F in mannosylfructose 6F-phosphate is used to indicate that the fructose residue of sucrose carries the substituent.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Torres, L.L. and Salerno, G.L. A metabolic pathway leading to mannosylfructose biosynthesis in Agrobacterium tumefaciens uncovers a family of mannosyltransferases. Proc. Natl. Acad. Sci. USA 104 (2007) 14318–14323. [PMID: 17728402]
[EC 3.1.3.79 created 2009]
 
 
*EC 3.2.1.97
Accepted name: endo-α-N-acetylgalactosaminidase
Reaction: β-D-galactosyl-(1→3)-N-acetyl-α-D-galactosaminyl-[glycoprotein]-L-serine/L-threonine + H2O = β-D-galactosyl-(1→3)-N-acetyl-D-galactosamine + [glycoprotein]-L-serine/L-threonine
Other name(s): endo-α-acetylgalactosaminidase; endo-α-N-acetyl-D-galactosaminidase; mucinaminylserine mucinaminidase; D-galactosyl-3-(N-acetyl-α-D-galactosaminyl)-L-serine mucinaminohydrolase; endo-α-GalNAc-ase; glycopeptide α-N-acetylgalactosaminidase; D-galactosyl-N-acetyl-α-D-galactosamine D-galactosyl-N-acetyl-galactosaminohydrolase
Systematic name: glycopeptide-D-galactosyl-N-acetyl-α-D-galactosamine D-galactosyl-N-acetyl-galactosaminohydrolase
Comments: The enzyme catalyses the liberation of Gal-(1→3)-β-GalNAc α-linked to serine or threonine residues of mucin-type glycoproteins. EngBF from the bacterium Bifidobacterium longum specifically acts on core 1-type O-glycan to release the disaccharide Gal-(1→3)-β-GalNAc. The enzymes from the bacteria Clostridium perfringens, Enterococcus faecalis, Propionibacterium acnes and Alcaligenes faecalis show broader specificity (e.g. they can also release the core 2 trisaccharide Gal-(1→3)-β-(GlcNAc-(1→6)-β)-GalNAc or the core 3 disaccharide GlcNAc-(1→3)-β-GalNAc) [1,2]. The enzyme may play an important role in the degradation and utilization of mucins having core 1 O-glycan.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 59793-96-3
References:
1.  Ashida, H., Maki, R., Ozawa, H., Tani, Y., Kiyohara, M., Fujita, M., Imamura, A., Ishida, H., Kiso, M. and Yamamoto, K. Characterization of two different endo-α-N-acetylgalactosaminidases from probiotic and pathogenic enterobacteria, Bifidobacterium longum and Clostridium perfringens. Glycobiology 18 (2008) 727–734. [PMID: 18559962]
2.  Koutsioulis, D., Landry, D. and Guthrie, E.P. Novel endo-α-N-acetylgalactosaminidases with broader substrate specificity. Glycobiology 18 (2008) 799–805. [PMID: 18635885]
3.  Fujita, K., Oura, F., Nagamine, N., Katayama, T., Hiratake, J., Sakata, K., Kumagai, H. and Yamamoto, K. Identification and molecular cloning of a novel glycoside hydrolase family of core 1 type O-glycan-specific endo-α-N-acetylgalactosaminidase from Bifidobacterium longum. J. Biol. Chem. 280 (2005) 37415–37422. [PMID: 16141207]
4.  Suzuki, R., Katayama, T., Kitaoka, M., Kumagai, H., Wakagi, T., Shoun, H., Ashida, H., Yamamoto, K. and Fushinobu, S. Crystallographic and mutational analyses of substrate recognition of endo-α-N-acetylgalactosaminidase from Bifidobacterium longum. J. Biochem. 146 (2009) 389–398. [PMID: 19502354]
5.  Gregg, K.J. and Boraston, A.B. Cloning, recombinant production, crystallization and preliminary X-ray diffraction analysis of a family 101 glycoside hydrolase from Streptococcus pneumoniae. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 133–135. [PMID: 19194003]
6.  Ashida, H., Yamamoto, K., Murata, T., Usui, T. and Kumagai, H. Characterization of endo-α-N-acetylgalactosaminidase from Bacillus sp. and syntheses of neo-oligosaccharides using its transglycosylation activity. Arch. Biochem. Biophys. 373 (2000) 394–400. [PMID: 10620364]
7.  Goda, H.M., Ushigusa, K., Ito, H., Okino, N., Narimatsu, H. and Ito, M. Molecular cloning, expression, and characterization of a novel endo-α-N-acetylgalactosaminidase from Enterococcus faecalis. Biochem. Biophys. Res. Commun. 375 (2008) 441–446. [PMID: 18725192]
[EC 3.2.1.97 created 1978 (EC 3.2.1.110 created 1984, incorporated 2008), modified 2008, modified 2011]
 
 
EC 3.2.1.110
Deleted entry: mucinaminylserine mucinaminidase. The enzyme is identical to EC 3.2.1.97, glycopeptide α-N-acetylgalactosaminidase
[EC 3.2.1.110 created 1984, deleted 2008]
 
 
EC 4.1.1.87
Accepted name: malonyl-S-ACP decarboxylase
Reaction: a malonyl-[acyl-carrier protein] + H+ = an acetyl-[acyl-carrier protein] + CO2
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): malonyl-S-acyl-carrier protein decarboxylase; MdcD/MdcE; MdcD,E
Systematic name: malonyl-[acyl-carrier-protein] carboxy-lyase
Comments: This enzyme comprises the β and γ subunits of EC 4.1.1.88 (biotin-independent malonate decarboxylase) but is not present in EC 4.1.1.89 (biotin-dependent malonate decarboxylase). It follows on from EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase, and results in the regeneration of the acetylated form of the acyl-carrier-protein subunit of malonate decarboxylase [5]. The carboxy group is lost with retention of configuration [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Schmid, M., Berg, M., Hilbi, H. and Dimroth, P. Malonate decarboxylase of Klebsiella pneumoniae catalyses the turnover of acetyl and malonyl thioester residues on a coenzyme-A-like prosthetic group. Eur. J. Biochem. 237 (1996) 221–228. [PMID: 8620876]
2.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [PMID: 10561613]
3.  Handa, S., Koo, J.H., Kim, Y.S. and Floss, H.G. Stereochemical course of biotin-independent malonate decarboxylase catalysis. Arch. Biochem. Biophys. 370 (1999) 93–96. [PMID: 10496981]
4.  Chohnan, S., Akagi, K. and Takamura, Y. Functions of malonate decarboxylase subunits from Pseudomonas putida. Biosci. Biotechnol. Biochem. 67 (2003) 214–217. [PMID: 12619701]
5.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 4.1.1.87 created 2008]
 
 
EC 4.1.1.88
Accepted name: biotin-independent malonate decarboxylase
Reaction: malonate + H+ = acetate + CO2
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): malonate decarboxylase (without biotin); malonate decarboxylase (ambiguous); MDC
Systematic name: malonate carboxy-lyase (biotin-independent)
Comments: Two types of malonate decarboxylase are currently known, both of which form multienzyme complexes. This enzyme is a cytosolic protein that is biotin-independent. The other type is a biotin-dependent, Na+-translocating enzyme that includes both soluble and membrane-bound components (cf. EC 4.1.1.89, biotin-dependent malonate decarboxylase). As free malonate is chemically rather inert, it has to be activated prior to decarboxylation. In both enzymes, this is achieved by exchanging malonate with an acetyl group bound to an acyl-carrier protiein (ACP), to form malonyl-ACP and acetate, with subsequent decarboxylation regenerating the acetyl-ACP. The ACP subunit of both enzymes differs from that found in fatty-acid biosynthesis by having phosphopantethine attached to a serine side-chain as 2-(5-triphosphoribosyl)-3-dephospho-CoA rather than as phosphopantetheine 4′-phosphate. The individual enzymes involved in carrying out the reaction of this enzyme complex are EC 2.3.1.187 (acetyl-S-ACP:malonate ACP transferase), EC 2.3.1.39 ([acyl-carrier-protein] S-malonyltransferase) and EC 4.1.1.87 (malonyl-S-ACP decarboxylase). The carboxy group is lost with retention of configuration [6].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Schmid, M., Berg, M., Hilbi, H. and Dimroth, P. Malonate decarboxylase of Klebsiella pneumoniae catalyses the turnover of acetyl and malonyl thioester residues on a coenzyme-A-like prosthetic group. Eur. J. Biochem. 237 (1996) 221–228. [PMID: 8620876]
2.  Byun, H.S. and Kim, Y.S. Subunit organization of bacterial malonate decarboxylases: the smallest δ subunit as an acyl-carrier protein. J. Biochem. Mol. Biol. 30 (1997) 132–137.
3.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [PMID: 9208947]
4.  Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37–43. [PMID: 9851033]
5.  Hoenke, S., Schmid, M. and Dimroth, P. Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases. Biochemistry 39 (2000) 13233–13240. [PMID: 11052676]
6.  Handa, S., Koo, J.H., Kim, Y.S. and Floss, H.G. Stereochemical course of biotin-independent malonate decarboxylase catalysis. Arch. Biochem. Biophys. 370 (1999) 93–96. [PMID: 10496981]
7.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [PMID: 10561613]
8.  Kim, Y.S. Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application. J. Biochem. Mol. Biol. 35 (2002) 443–451. [PMID: 12359084]
9.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 4.1.1.88 created 2008]
 
 
EC 4.1.1.89
Accepted name: biotin-dependent malonate decarboxylase
Reaction: malonate + H+ = acetate + CO2
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): malonate decarboxylase (with biotin); malonate decarboxylase (ambiguous)
Systematic name: malonate carboxy-lyase (biotin-dependent)
Comments: Two types of malonate decarboxylase are currently known, both of which form multienzyme complexes. The enzyme described here is a biotin-dependent, Na+-translocating enzyme that includes both soluble and membrane-bound components [6]. The other type is a biotin-independent cytosolic protein (cf. EC 4.1.1.88, biotin-independent malonate decarboxylase). As free malonate is chemically rather inert, it has to be activated prior to decarboxylation. Both enzymes achieve this by exchanging malonate with an acetyl group bound to an acyl-carrier protiein (ACP), to form malonyl-ACP and acetate, with subsequent decarboxylation regenerating the acetyl-bound form of the enzyme. The ACP subunit of both enzymes differs from that found in fatty-acid biosynthesis by having phosphopantethine attached to a serine side-chain as 2-(5-triphosphoribosyl)-3-dephospho-CoA rather than as phosphopantetheine 4′-phosphate. In the anaerobic bacterium Malonomonas rubra, the components of the multienzyme complex/enzymes involved in carrying out the reactions of this enzyme are as follows: MadA (EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase), MadB (EC 4.3.99.2, carboxybiotin decarboxylase), MadC/MadD (EC 2.1.3.10, malonyl-S-ACP:biotin-protein carboxyltransferase) and MadH (EC 6.2.1.35, ACP-SH:acetate ligase). Two other components that are involved are MadE, the acyl-carrier protein and MadF, the biotin protein. The carboxy group is lost with retention of configuration [5].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hilbi, H., Dehning, I., Schink, B. and Dimroth, P. Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme. Eur. J. Biochem. 207 (1992) 117–123. [PMID: 1628643]
2.  Hilbi, H. and Dimroth, P. Purification and characterization of a cytoplasmic enzyme component of the Na+-activated malonate decarboxylase system of Malonomonas rubra: acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase. Arch. Microbiol. 162 (1994) 48–56. [PMID: 18251085]
3.  Berg, M., Hilbi, H. and Dimroth, P. The acyl carrier protein of malonate decarboxylase of Malonomonas rubra contains 2′-(5"-phosphoribosyl)-3′-dephosphocoenzyme A as a prosthetic group. Biochemistry 35 (1996) 4689–4696. [PMID: 8664258]
4.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [PMID: 9128730]
5.  Micklefield, J., Harris, K.J., Gröger, S., Mocek, U., Hilbi, H., Dimroth, P. and Floss, H.G. Stereochemical course of malonate decarboxylase in Malonomonas rubra has biotin decarboxylation with retention. J. Am. Chem. Soc. 117 (1995) 1153–1154.
6.  Kim, Y.S. Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application. J. Biochem. Mol. Biol. 35 (2002) 443–451. [PMID: 12359084]
7.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 4.1.1.89 created 2008]
 
 
EC 4.2.3.37
Accepted name: epi-isozizaene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-epi-isozizaene + diphosphate
Other name(s): SCO5222 protein
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-epi-isozizaene-forming]
Comments: Requires Mg2+ for activity. The displacement of the diphosphate group of farnesyl diphosphate occurs with retention of configuration [1]. In the soil-dwelling bacterium Streptomyces coelicolor A3(2), the product of this reaction is used by EC 1.14.13.106, epi-isozizaene 5-monooxygenase, to produce the sesquiterpene antibiotic albaflavenone [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lin, X., Hopson, R. and Cane, D.E. Genome mining in Streptomyces coelicolor: molecular cloning and characterization of a new sesquiterpene synthase. J. Am. Chem. Soc. 128 (2006) 6022–6023. [PMID: 16669656]
2.  Zhao, B., Lin, X., Lei, L., Lamb, D.C., Kelly, S.L., Waterman, M.R. and Cane, D.E. Biosynthesis of the sesquiterpene antibiotic albaflavenone in Streptomyces coelicolor A3(2). J. Biol. Chem. 283 (2008) 8183–8189. [PMID: 18234666]
[EC 4.2.3.37 created 2008]
 
 
EC 4.3.99.2
Accepted name: carboxybiotin decarboxylase
Reaction: a carboxybiotinyl-[protein] + n Na+in + H+out = CO2 + a biotinyl-[protein] + n Na+out (n = 1–2)
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): MadB; carboxybiotin protein decarboxylase
Systematic name: carboxybiotinyl-[protein] carboxy-lyase
Comments: The integral membrane protein MadB from the anaerobic bacterium Malonomonas rubra is a component of the multienzyme complex EC 4.1.1.89, biotin-dependent malonate decarboxylase. The free energy of the decarboxylation reaction is used to pump Na+ out of the cell. The enzyme is a member of the Na+-translocating decarboxylase family, other members of which include EC 4.1.1.3 (oxaloacetate decarboxylase) and EC 4.1.1.41 (methylmalonyl-CoA decarboxylase) [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [PMID: 9128730]
2.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 4.3.99.2 created 2008]
 
 
EC 6.2.1.35
Accepted name: ACP-SH:acetate ligase
Reaction: ATP + acetate + an [acyl-carrier protein] = AMP + diphosphate + an acetyl-[acyl-carrier protein]
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): HS-acyl-carrier protein:acetate ligase; [acyl-carrier protein]:acetate ligase; MadH
Systematic name: acetate:[acyl-carrier-protein] ligase (AMP-forming)
Comments: This enzyme, from the anaerobic bacterium Malonomonas rubra, is a component of the multienzyme complex EC 4.1.1.89, biotin-dependent malonate decarboxylase. The enzyme uses the energy from hydrolysis of ATP to convert the thiol group of the acyl-carrier-protein-bound 2′-(5-phosphoribosyl)-3′-dephospho-CoA prosthetic group into its acetyl thioester [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hilbi, H., Dehning, I., Schink, B. and Dimroth, P. Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme. Eur. J. Biochem. 207 (1992) 117–123. [PMID: 1628643]
2.  Berg, M., Hilbi, H. and Dimroth, P. The acyl carrier protein of malonate decarboxylase of Malonomonas rubra contains 2′-(5"-phosphoribosyl)-3′-dephosphocoenzyme A as a prosthetic group. Biochemistry 35 (1996) 4689–4696. [PMID: 8664258]
3.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [PMID: 9128730]
4.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [PMID: 11902724]
[EC 6.2.1.35 created 2008]
 
 


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