Proposed Changes to the Enzyme List

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

Contents

Accepted name: tropinone reductase I

Reaction: tropine + NADP⁺ = tropinone + NADPH + H⁺

For diagram of reaction, click here

Glossary: tropine = 3α-hydroxytropane = tropan-3-endo-ol

Other name(s): tropine dehydrogenase; tropinone reductase (ambiguous); TR-I

Systematic name: tropine:NADP⁺ 3α-oxidoreductase

Comments: Also oxidizes other tropan-3α-ols, but not the corresponding β-derivatives [1]. This enzyme along with EC 1.1.1.236, tropinone reductase II, represents a branch point in tropane alkaloid metabolism [4]. Tropine (the product of EC 1.1.1.206) is incorporated into hyoscyamine and scopolamine whereas pseudotropine (the product of EC 1.1.1.236) is the first specific metabolite on the pathway to the calystegines [4]. Both enzymes are always found together in any given tropane-alkaloid-producing species, have a common substrate, tropinone, and are strictly stereospecific [3].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, PDB, CAS registry number: 118390-87-7

References:

1. Koelen, K.J. and Gross, G.G. Partial purification and properties of tropine dehydrogenase from root cultures of Datura stramonium. Planta Med. 44 (1982) 227-230.

2. Couladis, M.M, Friesen, J.B., Landgrebe, M.E. and Leete, E. Enzymes catalysing the reduction of tropinone to tropine and ψ-tropine isolated from the roots of Datura innoxia. Pytochemistry 30 (1991) 801-805.

3. Nakajima, K., Hashimoto, T. and Yamada, Y. Two tropinone reductases with different stereospecificities are short-chain dehydrogenases evolved from a common ancestor. Proc. Natl. Acad. Sci. USA 90 (1993) 9591-9595. [PMID: 8415746]

4. Dräger, B. Tropinone reductases, enzymes at the branch point of tropane alkaloid metabolism. Phytochemistry 67 (2006) 327-337. [PMID: 16426652]

*EC 1.1.1.236

Accepted name: tropinone reductase II

Reaction: pseudotropine + NADP⁺ = tropinone + NADPH + H⁺

For diagram of reaction, click here

Glossary: pseudotropine = ψ-tropine = 3β-hydroxytropane = tropan-3-exo-ol

Other name(s): tropinone (ψ-tropine-forming) reductase; pseudotropine forming tropinone reductase; tropinone reductase (ambiguous); TR-II

Systematic name: pseudotropine:NADP⁺ 3-oxidoreductase

Comments: This enzyme along with EC 1.1.1.206, tropinone reductase I, represents a branch point in tropane alkaloid metabolism [3]. Tropine (the product of EC 1.1.1.206) is incorporated into hyoscyamine and scopolamine whereas pseudotropine (the product of EC 1.1.1.236) is the first specific metabolite on the pathway to the calystegines [3]. Both enzymes are always found together in any given tropane-alkaloid-producing species, have a common substrate, tropinone, and are strictly stereospecific [2].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, PDB, CAS registry number: 136111-61-0

References:

1. Dräger, B., Hashimoto, T. and Yamada, Y. Purification and characterization of pseudotropine forming tropinone reductase from Hyoscyamus niger root cultures. Agric. Biol. Chem. 52 (1988) 2663-2667.

2. Couladis, M.M, Friesen, J.B., Landgrebe, M.E. and Leete, E. Enzymes catalysing the reduction of tropinone to tropine and ψ-tropine isolated from the roots of Datura innoxia. Pytochemistry 30 (1991) 801-805.

3. Nakajima, K., Hashimoto, T. and Yamada, Y. Two tropinone reductases with different stereospecificities are short-chain dehydrogenases evolved from a common ancestor. Proc. Natl. Acad. Sci. USA 90 (1993) 9591-9595. [PMID: 8415746]

4. Dräger, B. Tropinone reductases, enzymes at the branch point of tropane alkaloid metabolism. Phytochemistry 67 (2006) 327-337. [PMID: 16426652]

[EC 1.1.1.293 Deleted entry: tropinone reductase I. This enzyme was already in the Enzyme List as EC 1.1.1.206, tropine dehydrogenase so EC 1.1.1.293 has been withdrawn at the public-review stage. (EC 1.1.1.293 created 2007, withdrawn while undergoing public review)]

EC 1.1.1.294

Accepted name: chlorophyll(ide) b reductase

Reaction: 7¹-hydroxychlorophyllide a + NAD(P)⁺ = chlorophyllide b + NAD(P)H + H⁺

Other name(s): chlorophyll b reductase; Chl b reductase

Systematic name: 7¹-hydroxychlorophyllide-a:NAD(P)⁺ oxidoreductase

Comments: This enzyme carries out the first step in the conversion of chlorophyll b to chlorophyll a. It is involved in chlorophyll degradation, which occurs during leaf senescence [3,4] and it also forms part of the chlorophyll cycle, which interconverts chlorophyll a and b in response to changing light conditions [5,6]. While both chlorophyll a and chlorophyll b are found in higher plants, only breakdown products derived from chlorophyll a are found in the end products, i.e. non-fluorescent chlorophyll catabolites (NCCs). The transition from chlorophyll b, which contains a formyl group on C7, to chlorophyll a, which contains a methyl group on C7, proceeds through the intermediate 7¹-hydroxychlorophyll [1]. Another enzyme, which requires ferredoxin but has not been characterized fully, is required to complete the conversion [3].

References:

1. Scheumann, V., Ito, H., Tanaka, A., Schoch, S. and Rüdiger, W. Substrate specificity of chlorophyll(ide) b reductase in etioplasts of barley (Hordeum vulgare L.). Eur. J. Biochem. 242 (1996) 163-170. [PMID: 8954166]

2. Scheumann, V., Schoch, S. and Rüdiger, W. Chlorophyll a formation in the chlorophyll b reductase reaction requires reduced ferredoxin. J. Biol. Chem. 273 (1998) 35102-35108. [PMID: 9857045]

3. Scheumann, V., V., Schoch, S. and Rüdiger, W. Chlorophyll b reduction during senescence of barley seedling. Planta 209 (1999) 364-370. [PMID: 10502104]

4. Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55-77. [PMID: 16669755]

5. Ito, H., Ohtsuka, T. and Tanaka, A. Conversion of chlorophyll b to chlorophyll a via 7-hydroxymethyl chlorophyll. J. Biol. Chem. 271 (1996) 1475-1479. [PMID: 8576141]

6. Rüdiger, W. Biosynthesis of chlorophyll b and the chlorophyll cycle. Photosynth. Res. 74 (2002) 187-193. [PMID: 16228557]

*EC 1.1.3.17

Accepted name: choline oxidase

Reaction: choline + 2 O₂ + H₂O = betaine + 2 H₂O₂ (overall reaction)
(1a) choline + O₂ = betaine aldehyde + H₂O₂
(1b) betaine aldehyde + O₂ + H₂O = betaine + H₂O₂

Glossary: choline = (2-hydroxyethyl)trimethylammonium
betaine aldehyde = N,N,N-trimethyl-2-oxoethylammonium
betaine = glycine betaine = N,N,N-trimethylammonioacetate

Systematic name: choline:oxygen 1-oxidoreductase

Comments: A flavoprotein (FAD). In many bacteria, plants and animals, the osmoprotectant betaine is synthesized using different enzymes to catalyse the conversion of (1) choline into betaine aldehyde and (2) betaine aldehyde into betaine. In plants, the first reaction is catalysed by EC 1.14.15.7EC 1.14.15.7, choline monooxygenase, whereas in animals and many bacteria, it is catalysed by either membrane-bound choline dehydrogenase (EC 1.1.99.1) or soluble choline oxidase (EC 1.1.3.17) [6]. The enzyme involved in the second step, EC 1.2.1.8, betaine-aldehyde dehydrogenase, appears to be the same in those plants, animals and bacteria that use two separate enzymes.

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, CAS registry number: 9028-67-5

References:

1. Ikuta, S., Imamura, S., Misaki, H. and Horiuti, Y. Purification and characterization of choline oxidase from Arthrobacter globiformis. J. Biochem. (Tokyo) 82 (1977) 1741-1749. [PMID: 599154]

2. Rozwadowski, K.L., Khachatourians, G.G. and Selvaraj, G. Choline oxidase, a catabolic enzyme in Arthrobacter pascens, facilitates adaptation to osmotic stress in Escherichia coli. J. Bacteriol. 173 (1991) 472-478. [PMID: 1987142]

3. Rand, T., Halkier, T. and Hansen, O.C. Structural characterization and mapping of the covalently linked FAD cofactor in choline oxidase from Arthrobacter globiformis. Biochemistry 42 (2003) 7188-7194. [PMID: 12795615]

4. Gadda, G., Powell, N.L. and Menon, P. The trimethylammonium headgroup of choline is a major determinant for substrate binding and specificity in choline oxidase. Arch. Biochem. Biophys. 430 (2004) 264-273. [PMID: 15369826]

5. Fan, F. and Gadda, G. On the catalytic mechanism of choline oxidase. J. Am. Chem. Soc. 127 (2005) 2067-2074. [PMID: 15713082]

6. Waditee, R., Tanaka, Y., Aoki, K., Hibino, T., Jikuya, H., Takano, J., Takabe, T. and Takabe, T. Isolation and functional characterization of N-methyltransferases that catalyze betaine synthesis from glycine in a halotolerant photosynthetic organism Aphanothece halophytica. J. Biol. Chem. 278 (2003) 4932-4942. [PMID: 12466265]

7. Fan, F., Ghanem, M. and Gadda, G. Cloning, sequence analysis, and purification of choline oxidase from Arthrobacter globiformis: a bacterial enzyme involved in osmotic stress tolerance. Arch. Biochem. Biophys. 421 (2004) 149-158. [PMID: 14678796]

8. Gadda, G. Kinetic mechanism of choline oxidase from Arthrobacter globiformis. Biochim. Biophys. Acta 1646 (2003) 112-118. [PMID: 12637017]

*EC 1.2.1.19

Accepted name: aminobutyraldehyde dehydrogenase

Reaction: 4-aminobutanal + NAD⁺ + H₂O = 4-aminobutanoate + NADH + 2 H⁺

For diagram click here.

Other name(s): ABAL dehydrogenase; 4-aminobutyraldehyde dehydrogenase; 4-aminobutanal dehydrogenase; γ-aminobutyraldehyde dehydroganase; 1-pyrroline dehydrogenase; ABALDH; YdcW; γ-guanidinobutyraldehyde dehydrogenase (ambiguous)

Systematic name: 4-aminobutanal:NAD⁺ 1-oxidoreductase

Comments: The enzyme from some species exhibits broad substrate specificity and has a marked preference for straight-chain aldehydes (up to 7 carbon atoms) as substrates [9]. The plant enzyme also acts on 4-guanidinobutanal (cf. EC 1.2.1.54 γ-guanidinobutyraldehyde dehydrogenase). As 1-pyrroline and 4-aminobutanal are in equilibrium and can be interconverted spontaneously, 1-pyrroline may act as the starting substrate. The enzyme forms part of the arginine-catabolism pathway [8] and belongs in the aldehyde dehydrogenase superfamily [9].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, CAS registry number: 9028-98-2

References:

1. Callewaert, D.M., Rosemblatt, M.S. and Tchen, T.T. Purification and properties of 4-aminobutanal dehydrogenase from a Pseudomonas species. J. Biol. Chem. 249 (1974) 1737-1741. [PMID: 4817964]

2. Jakoby, W.B. Aldehyde dehydrogenases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 203-221.

3. Jakoby, W.B. and Fredericks, J. Pyrrolidine and putrescine metabolism: γ-aminobutyraldehyde dehydrogenase. J. Biol. Chem. 234 (1959) 2145-2150. [PMID: 13673029]

4. Matsuda, H. and Suzuki, Y. γ-Guanidinobutyraldehyde dehydrogenase of Vicia faba leaves. Plant Physiol. 76 (1984) 654-657. [PMID: 16663901]

5. Yorifuji, T., Koike, K., Sakurai, T. and Yokoyama, K. 4-Aminobutyraldehyde and 4-guanidinobutyraldehyde dehydrogenases for arginine degradation in Pseudomonas putida. Agric. Biol. Chem. 50 (1986) 2009-2016.

6. Prieto-Santos, M.I., Martin-Checa, J., Balaña-Fouce, R. and Garrido-Pertierra, A. A pathway for putrescine catabolism in Escherichia coli. Biochim. Biophys. Acta 880 (1986) 242-244. [PMID: 3510672]

7. Prieto, M.I., Martin, J., Balaña-Fouce, R. and Garrido-Pertierra, A. Properties of γ-aminobutyraldehyde dehydrogenase from Escherichia coli. Biochimie 69 (1987) 1161-1168. [PMID: 3129020]

8. Samsonova, N.N., Smirnov, S.V., Novikova, A.E. and Ptitsyn, L.R. Identification of Escherichia coli K12 YdcW protein as a γ-aminobutyraldehyde dehydrogenase. FEBS Lett. 579 (2005) 4107-4112. [PMID: 16023116]

9. Gruez, A., Roig-Zamboni, V., Grisel, S., Salomoni, A., Valencia, C., Campanacci, V., Tegoni, M. and Cambillau, C. Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase. J. Mol. Biol. 343 (2004) 29-41. [PMID: 15381418]

*EC 1.3.1.53

Accepted name: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate dehydrogenase

Reaction: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD⁺ = 3,4-dihydroxybenzoate + CO₂ + NADH

Glossary: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate = cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,4-dicarboxylate

Other name(s): (1R,2S)-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase; terephthalate 1,2-cis-dihydrodiol dehydrogenase; cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,4-dicarboxylate:NAD⁺ oxidoreductase (decarboxylating)

Systematic name: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate:NAD⁺ oxidoreductase

Comments: Requires Fe^II. Involved in the terephthalate degradation pathway in bacteria [2].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, CAS registry number: 162032-77-1

References:

1. Saller, E., Laue, H.R., Schläfli Oppenberg, H.R. and Cook, A.M. Purification and some properties of (1R,2S)-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase from Comamonas testosteroni T-2. FEMS Microbiol. Lett. 130 (1996) 97-102.

2. Wang, Y.Z., Zhou, Y. and Zylstra, G.J. Molecular analysis of isophthalate and terephthalate degradation by Comamonas testosteroni YZW-D. Environ. Health Perspect. 103, Suppl. 5 (1995) 9-12. [PMID: 8565920]

[EC 1.3.1.61 Deleted entry: terephthalate 1,2-cis-dihydrodiol dehydrogenase. Enzyme is identical to EC 1.3.1.53, (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate dehydrogenase. (EC 1.3.1.61 created 2000, deleted 2007)]

EC 1.3.1.80

Accepted name: red chlorophyll catabolite reductase

Reaction: primary fluorescent chlorophyll catabolite + NADP⁺ = red chlorophyll catabolite + NADPH + H⁺

For diagram click here

Glossary: red chlorophyll catabolite = RCC = (7S,8S,10¹R)-8-(2-carboxyethyl)-17-ethyl-19-formyl-10¹-(methoxycarbonyl)-3,7,13,18-tetramethyl-2-vinyl-8,23-dihydro-7H-10,12-ethanobiladiene-ab-1,10²(21H)-dione
primary fluorescent chlorophyll catabolite = pFCC = (8²R,12S,13S)-12-(2-carboxyethyl)-3-ethyl-1-formyl-8²-(methoxycarbonyl)-2,7,13,17-tetramethyl-18-vinyl-12,13-dihydro-8,10-ethanobilene-b-8¹,19(16H)-dione

Other name(s): RCCR; RCC reductase; red Chl catabolite reductase

Systematic name: primary fluorescent chlorophyll catabolite:NADP⁺ oxidoreductase

Comments: Chlorophyll degradation is a characteristic symptom of leaf senescence and fruit ripening. The reaction catalysed by this enzyme requires reduced ferredoxin, which is generated either by NADPH through the pentose-phosphate pathway or by the action of photosystem I [1,2]. This reaction takes place without release of the substrate from EC 1.14.12.20, pheophorbide a oxygenase [3]. Depending on the plant species used as the source of enzyme, one of two possible C-1 epimers of primary fluorescent chlorophyll catabolite (pFCC), pFCC-1 or pFCC-2, is normally formed, with all genera or species within a family producing the same isomer [3,4]. After modification and export, pFCCs are eventually imported into the vacuole, where the acidic environment causes their non-enzymic conversion into colourless breakdown products called non-fluorescent chlorophyll catabolites (NCCs) [2].

References:

1. Rodoni, S., Mühlecker, W., Anderl, M., Kräutler, B., Moser, D., Thomas, H., Matile, P. and Hörtensteiner, S. Chlorophyll breakdown in senescent chloroplasts. Cleavage of pheophorbide a in two enzymic steps. Plant Physiol. 115 (1997) 669-676. [PMID: 12223835]

2. Wüthrich, K.L., Bovet, L., Hunziker, P.E., Donnison, I.S. and Hörtensteiner, S. Molecular cloning, functional expression and characterisation of RCC reductase involved in chlorophyll catabolism. Plant J. 21 (2000) 189-198. [PMID: 10743659]

3. Pružinská, A., Anders, I., Aubry, S., Schenk, N., Tapernoux-Lüthi, E., Müller, T., Kräutler, B. and Hörtensteiner, S. In vivo participation of red chlorophyll catabolite reductase in chlorophyll breakdown. Plant Cell 19 (2007) 369-387. [PMID: 17237353]

4. Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55-77. [PMID: 16669755]

5. Rodoni, S., Vicentini, F., Schellenberg, M., Matile, P. and Hörtensteiner, S. Partial purification and characterization of red chlorophyll catabolite reductase, a stroma protein involved in chlorophyll breakdown. Plant Physiol. 115 (1997) 677-682. [PMID: 12223836]

Note: For reference 1 an accent may not be seen. ž is z-hacek

[EC 1.5.1.35 Deleted entry: 1-pyrroline dehydrogenase. The enzyme is identical to EC 1.2.1.19, aminobutyraldehyde dehydrogenase, as the substrates 1-pyrroline and 4-aminobutanal are interconvertible. (EC 1.5.1.35 created 2006, deleted 2007)]

EC 1.14.12.20

Accepted name: pheophorbide a oxygenase

Reaction: pheophorbide a + NADPH + H⁺ + O₂ = red chlorophyll catabolite + NADP⁺

For diagram click here and for mechanism click here.

Glossary: red chlorophyll catabolite = RCC = (7S,8S,10¹R)-8-(2-carboxyethyl)-17-ethyl-19-formyl-10¹-(methoxycarbonyl)-3,7,13,18-tetramethyl-2-vinyl-8,23-dihydro-7H-10,12-ethanobiladiene-ab-1,10²(21H)-dione

Other name(s): pheide a monooxygenase; pheide a oxygenase; PaO; PAO

Systematic name: pheophorbide-a,NADPH:oxygen oxidoreductase (biladiene-forming)

Comments: This enzyme catalyses a key reaction in chlorophyll degradation, which occurs during leaf senescence and fruit ripening in higher plants. The enzyme from Arabidopsis contains a Rieske-type iron-sulfur cluster [2] and requires reduced ferredoxin, which is generated either by NADPH through the pentose-phosphate pathway or by the action of photosystem I [4]. While still attached to this enzyme, the product is rapidly converted into primary fluorescent chlorophyll catabolite by the action of EC 1.3.1.80, red chlorophyll catabolite reductase [2,6]. Pheophorbide b acts as an inhibitor. In ¹⁸O₂ labelling experiments, only the aldehyde oxygen is labelled, suggesting that the other oxygen atom may originate from H₂O [1].

References:

1. Hörtensteiner, S., Wüthrich, K.L., Matile, P., Ongania, K.H. and Kräutler, B. The key step in chlorophyll breakdown in higher plants. Cleavage of pheophorbide a macrocycle by a monooxygenase. J. Biol. Chem. 273 (1998) 15335-15339. [PMID: 9624113]

2. Pružinská, A., Tanner, G., Anders, I., Roca, M. and Hörtensteiner, S. Chlorophyll breakdown: pheophorbide a oxygenase is a Rieske-type iron-sulfur protein, encoded by the accelerated cell death 1 gene. Proc. Natl. Acad. Sci. USA 100 (2003) 15259-15264. [PMID: 14657372]

3. Chung, D.W., Pružinská, A., Hörtensteiner, S. and Ort, D.R. The role of pheophorbide a oxygenase expression and activity in the canola green seed problem. Plant Physiol. 142 (2006) 88-97. [PMID: 16844830]

4. Rodoni, S., Mühlecker, W., Anderl, M., Kräutler, B., Moser, D., Thomas, H., Matile, P. and Hörtensteiner, S. Chlorophyll breakdown in senescent chloroplasts. Cleavage of pheophorbide a in two enzymic steps. Plant Physiol. 115 (1997) 669-676. [PMID: 12223835]

5. Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55-77. [PMID: 16669755]

6. Pružinská, A., Anders, I., Aubry, S., Schenk, N., Tapernoux-Lüthi, E., Müller, T., Kräutler, B. and Hörtensteiner, S. In vivo participation of red chlorophyll catabolite reductase in chlorophyll breakdown. Plant Cell 19 (2007) 369-387. [PMID: 17237353]

Note: For reference 2 and 3 an accent may not be seen. ž is z-hacek

EC 1.14.13.102

Accepted name: psoralen synthase

Reaction: (+)-marmesin + NADPH + H⁺ + O₂ = psoralen + NADP⁺ + acetone + 2 H₂O

For diagram of reaction, click here

Glossary: (+)-marmesin = (S)-2-(2-hydroxypropan-2-yl)-2H-furo[3,2-g]chromen-7(3H)-one
psoralen = 7H-furo[3,2-g]chromen-7-one

Other name(s): CYP71AJ1

Comments: This microsomal cytochrome P₄₅₀-dependent enzyme is specific for (+)-marmesin, and to a much lesser extent 5-hydroxymarmesin, as substrate. Furanocoumarins protect plants from fungal invasion and herbivore attack. (+)-Columbianetin, the angular furanocoumarin analogue of the linear furanocoumarin (+)-marmesin, is not a substrate for the enzyme but it is a competitive inhibitor.

References:

1. Larbat, R., Kellner, S., Specker, S., Hehn, A., Gontier, E., Hans, J., Bourgaud, F. and Matern, U. Molecular cloning and functional characterization of psoralen synthase, the first committed monooxygenase of furanocoumarin biosynthesis. J. Biol. Chem. 282 (2007) 542-554. [PMID: 17068340]

EC 1.14.13.103

Accepted name: 8-dimethylallylnaringenin 2'-hydroxylase

Reaction: sophoraflavanone B + NADPH + H⁺ + O₂ = leachianone G + NADP⁺ + H₂O

For diagram of reaction, click here

Glossary: sophoraflavanone B = (–)-(2S)-8-dimethylallylnaringenin = (–)-(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-enyl)chroman-4-one
leachianone G = (–)-(2S)-2'-hydroxy-8-dimethylallylnaringenin = (–)-(2S)-5,7-dihydroxy-8-(2-hydroxy-3-methylbut-2-enyl)-2-(4-hydroxyphenyl)chroman-4-one

Other name(s): 8-DMAN 2'-hydroxylase

Systematic name: sophoraflavanone-B,NADPH:oxygen oxidoreductase (2'-hydroxylating)

Comments: A membrane-bound heme-thiolate protein that is associated with the endoplasmic reticulum [1,2]. This enzyme is specific for sophoraflavanone B as substrate. NADPH cannot be replaced by NADH, FAD or FMN. Along with EC 2.5.1.70 (naringenin 8-dimethylallyltransferase) and EC 2.5.1.71 (leachianone G 2"-dimethylallyltransferase), this enzyme forms part of the sophoraflavanone-G-biosynthesis pathway. A member of the cytochrome-P₄₅₀ monooxygenase family.

References:

1. Yamamoto, H., Yatou, A. and Inoue, K. 8-Dimethylallylnaringenin 2′-hydroxylase, the crucial cytochrome P₄₅₀ mono-oxygenase for lavandulylated flavanone formation in Sophora flavescens cultured cells. Phytochemistry 58 (2001) 671-676. [PMID: 11672730]

2. Zhao, P., Inoue, K., Kouno, I. and Yamamoto, H. Characterization of leachianone G 2"-dimethylallyltransferase, a novel prenyl side-chain elongation enzyme for the formation of the lavandulyl group of sophoraflavanone G in Sophora flavescens Ait. cell suspension cultures. Plant Physiol. 133 (2003) 1306-1313. [PMID: 14551337]

EC 2.1.1.161

Accepted name: dimethylglycine N-methyltransferase

Reaction: S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine

Glossary: betaine = glycine betaine = N,N,N-trimethylglycine

Other name(s): BsmB; DMT

Systematic name: S-adenosyl-L-methionine:N,N-dimethylglycine N-methyltransferase (betaine-forming)

Comments: This enzyme, from the marine cyanobacterium Synechococcus sp. WH8102, differs from 2.1.1.157, sarcosine/dimethylglycine N-methyltransferase in that it cannot use sarcosine as an alternative substrate [1]. Betaine is a 'compatible solute' that enables cyanobacteria to cope with osmotic stress by maintaining a positive cellular turgor.

References:

1. Lu, W.D., Chi, Z.M. and Su, C.D. Identification of glycine betaine as compatible solute in Synechococcus sp. WH8102 and characterization of its N-methyltransferase genes involved in betaine synthesis. Arch. Microbiol. 186 (2006) 495-506. [PMID: 17019606]

EC 2.1.1.162

Accepted name: glycine/sarcosine/dimethylglycine N-methyltransferase

Reaction: (1) S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
(2) S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine
(3) S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine

Glossary: sarcosine = N-methylglycine
betaine = glycine betaine = N,N,N-trimethylglycine

Other name(s): GSDMT; glycine sarcosine dimethylglycine N-methyltransferase

Systematic name: S-adenosyl-L-methionine:glycine(or sarcosine or N,N-dimethylglycine) N-methyltransferase [sarcosine(or N,N-dimethylglycine or betaine)-forming]

Comments: Unlike EC 2.1.1.156 (glycine/sarcosine N-methyltransferase), EC 2.1.1.157 (sarcosine/dimethylglycine N-methyltransferase) and EC 2.1.1.161 (dimethylglycine N-methyltransferase), this enzyme, from the halophilic methanoarchaeon Methanohalophilus portucalensis, can methylate glycine and all of its intermediates to form the compatible solute betaine [1].

References:

1. Lai, M.C., Wang, C.C., Chuang, M.J., Wu, Y.C. and Lee, Y.C. Effects of substrate and potassium on the betaine-synthesizing enzyme glycine sarcosine dimethylglycine N-methyltransferase from a halophilic methanoarchaeon Methanohalophilus portucalensis. Res. Microbiol. 157 (2006) 948-955. [PMID: 17098399]

EC 2.3.1.182

Accepted name: (R)-citramalate synthase

Reaction: acetyl-CoA + pyruvate = CoA + (2R)-2-hydroxy-2-methylbutanedioate

Glossary: (–)-citramalate = (2R)-2-methylmalate = (2R)-2-hydroxy-2-methylbutanedioate
α-ketoisovalerate = 3-methyl-2-oxobutanoate
α-ketobutyrate = 2-oxobutanoate
α-ketoisocaproate = 4-methyl-2-oxopentanoate
α-ketopimelate = 2-oxohexanoate
α-ketoglutarate = 2-oxoglutarate

Other name(s): CimA

Comments: One of the enzymes involved in a novel pyruvate pathway for isoleucine biosynthesis that is found in some, mainly archaeal, bacteria [1,2]. The enzyme can be inhibited by isoleucine, the end-product of the pathway, but not by leucine [2]. The enzyme is highly specific for pyruvate as substrate, as the 2-oxo acids 3-methyl-2-oxobutanoate, 2-oxobutanoate, 4-methyl-2-oxopentanoate, 2-oxohexanoate and 2-oxoglutarate cannot act as substrate [1,2].

References:

1. Howell, D.M., Xu, H. and White, R.H. (R)-Citramalate synthase in methanogenic archaea. J. Bacteriol. 181 (1999) 331-333. [PMID: 9864346]

2. Xu, H., Zhang, Y., Guo, X., Ren, S., Staempfli, A.A., Chiao, J., Jiang, W. and Zhao, G. Isoleucine biosynthesis in Leptospira interrogans serotype 1ai strain 56601 proceeds via a threonine-independent pathway. J. Bacteriol. 186 (2004) 5400-5409. [PMID: 15292141]

EC 2.3.1.183

Accepted name: phosphinothricin acetyltransferase

Reaction: acetyl-CoA + phosphinothricin = CoA + N-acetylphosphinothricin

Glossary: phosphinothricin = glufosinate = 2-amino-4-[hydroxy(methyl)phosphoryl]butanoate

Other name(s): PAT; PPT acetyltransferase; Pt-N-acetyltransferase; ac-Pt

Systematic name: acetyl-CoA:phosphinothricin N-acetyltransferase

Comments: The substrate phosphinothricin is used as a nonselective herbicide and is a potent inhibitor of EC 6.3.1.2, glutamate—ammonia ligase, a key enzyme of nitrogen metabolism in plants [2].

References:

1. Botterman, J., Gosselé, V., Thoen, C. and Lauwereys, M. Characterization of phosphinothricin acetyltransferase and C-terminal enzymatically active fusion proteins. Gene 102 (1991) 33-37. [PMID: 1864506]

2. Dröge-Laser, W., Siemeling, U., Pühler, A. and Broer, I. The metabolites of the herbicide L-phosphinothricin (glufosinate) (identification, stability, and mobility in transgenic, herbicide-resistant, and untransformed plants). Plant Physiol. 105 (1994) 159-166. [PMID: 12232195]

EC 2.3.1.184

Accepted name: acyl-homoserine-lactone synthase

Reaction: an acyl-[acyl-carrier-protein] + S-adenosyl-L-methionine = [acyl-carrier-protein] + S-methyl-5'-thioadenosine + an N-acyl-L-homoserine lactone

For diagram click here

Other name(s): acyl-homoserine lactone synthase; acyl homoserine lactone synthase; acyl-homoserinelactone synthase; acylhomoserine lactone synthase; AHL synthase; AHS; AHSL synthase; AhyI; AinS; AinS protein; autoinducer synthase; autoinducer synthesis protein rhlI; EsaI; ExpISCC1; ExpISCC3065; LasI; LasR; LuxI; LuxI protein; LuxM; N-acyl homoserine lactone synthase; RhlI; YspI

Systematic name: acyl-[acyl carrier protein]:S-adenosyl-L-methionine acyltranserase (lactone-forming, methylthioadenosine-releasing)

Comments: Acyl-homoserine lactones (AHLs) are produced by a number of bacterial species and are used by them to regulate the expression of virulence genes in a process known as quorum-sensing. Each bacterial cell has a basal level of AHL and, once the population density reaches a critical level, it triggers AHL-signalling which, in turn, initiates the expression of particular virulence genes [5]. N-(3-Oxohexanoyl)-[acyl-carrier-protein] and hexanoyl-[acyl-carrier-protein] are the best substrates [1]. The fatty-acyl substrate is derived from fatty-acid biosynthesis through acyl-[acyl-carrier-protein] rather than from fatty-acid degradation through acyl-CoA [1]. S-Adenosyl-L-methionine cannot be replaced by methionine, S-adenosylhomocysteine, homoserine or homoserine lactone [1].

References:

1. Schaefer, A.L., Val, D.L., Hanzelka, B.L., Cronan, J.E., Jr. and Greenberg, E.P. Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein. Proc. Natl. Acad. Sci. USA 93 (1996) 9505-9509. [PMID: 8790360]

2. Watson, W.T., Murphy, F.V., 4th, Gould, T.A., Jambeck, P., Val, D.L., Cronan, J.E., Jr., Beck von Bodman, S. and Churchill, M.E. Crystallization and rhenium MAD phasing of the acyl-homoserinelactone synthase EsaI. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 1945-1949. [PMID: 11717525]

3. Chakrabarti, S. and Sowdhamini, R. Functional sites and evolutionary connections of acylhomoserine lactone synthases. Protein Eng. 16 (2003) 271-278. [PMID: 12736370]

4. Hanzelka, B.L., Parsek, M.R., Val, D.L., Dunlap, P.V., Cronan, J.E., Jr. and Greenberg, E.P. Acylhomoserine lactone synthase activity of the Vibrio fischeri AinS protein. J. Bacteriol. 181 (1999) 5766-5770. [PMID: 10482519]

5. Parsek, M.R., Val, D.L., Hanzelka, B.L., Cronan, J.E., Jr. and Greenberg, E.P. Acyl homoserine-lactone quorum-sensing signal generation. Proc. Natl. Acad. Sci. USA 96 (1999) 4360-4365. [PMID: 10200267]

6. Ulrich, R.L. Quorum quenching: enzymatic disruption of N-acylhomoserine lactone-mediated bacterial communication in Burkholderia thailandensis. Appl. Environ. Microbiol. 70 (2004) 6173-6180. [PMID: 15466564]

7. Gould, T.A., Schweizer, H.P. and Churchill, M.E. Structure of the Pseudomonas aeruginosa acyl-homoserinelactone synthase LasI. Mol. Microbiol. 53 (2004) 1135-1146. [PMID: 15306017]

8. Raychaudhuri, A., Jerga, A. and Tipton, P.A. Chemical mechanism and substrate specificity of RhlI, an acylhomoserine lactone synthase from Pseudomonas aeruginosa. Biochemistry 44 (2005) 2974-2981. [PMID: 15723540]

9. Gould, T.A., Herman, J., Krank, J., Murphy, R.C. and Churchill, M.E. Specificity of acyl-homoserine lactone synthases examined by mass spectrometry. J. Bacteriol. 188 (2006) 773-783. [PMID: 16385066]

*EC 2.4.2.29

Accepted name: tRNA-guanine transglycosylase

Reaction: (1) [tRNA]-guanine + queuine = [tRNA]-queuine + guanine
(2) [tRNA]-guanine + 7-aminomethyl-7-carbaguanine = [tRNA]-7-aminomethyl-7-carbaguanine + guanine

For diagram click here.

Glossary: preQ₁ = 7-aminomethyl-7-carbaguanine
preQ₀ = 7-cyano-7-carbaguanine
queuine = base Q = 22-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydropyrrolo[3,2-e]pyrimidin-4-one

Other name(s): guanine insertion enzyme; tRNA transglycosylase; Q-insertase; queuine transfer ribonucleate ribosyltransferase; transfer ribonucleate glycosyltransferase; tRNA guanine transglycosidase; guanine, queuine-tRNA transglycosylase; queuine tRNA-ribosyltransferase; TGT; [tRNA]-guanine:queuine tRNA-D-ribosyltransferase; transfer ribonucleic acid guanine transglycosylase

Systematic name: tRNA-guanine:queuine tRNA-D-ribosyltransferase

Comments: In eukaryotes, queuine is incorporated into tRNA directly via a base-exchange reaction (replacing guanine) whereas in eubacteria, the queuine precursor preQ₁ is incorporated and ultimately modified to queuine [4]. In eubacteria, preQ₀ can also be incorporated into undermodified tRNA^Tyr and tRNA^Asn containing normal guanine instead of queuine in the first position of the anticodon [2]. This enzyme acts after EC 1.7.1.13, preQ₁ synthase, in the queuine-biosynthesis pathway.

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, PDB, CAS registry number: 72162-89-1

References:

1. Howes, N.K. and Farkas, W.R. Studies with a homogeneous enzyme from rabbit erythrocytes catalyzing the insertion of guanine into tRNA. J. Biol. Chem. 253 (1978) 9082-9087. [PMID: 721832]

2. Okada, N., Noguchi, S., Kasai, H., Shindo-Okada, N., Ohgi, T., Goto, T. and Nishimura, S. Novel mechanism of post-transcriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. J. Biol. Chem. 254 (1979) 3067-3073. [PMID: 372186]

3. Shindo-Okada, N., Okada, N., Ohgi, T., Goto, T. and Nishimura, S. Transfer ribonucleic acid guanine transglycosylase isolated from rat liver. Biochemistry 19 (1980) 395-400. [PMID: 6986171]

4. Todorov, K.A. and Garcia, G.A. Role of aspartate 143 in Escherichia coli tRNA-guanine transglycosylase: alteration of heterocyclic substrate specificity. Biochemistry 45 (2006) 617-625. [PMID: 16401090]

EC 2.5.1.70

Accepted name: naringenin 8-dimethylallyltransferase

Reaction: dimethylallyl diphosphate + (–)-(2S)-naringenin = diphosphate + sophoraflavanone B

For diagram of reaction, click here

Glossary: (–)-(2S)-naringenin = (–)-(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one
sophoraflavanone B = (–)-(2S)-8-dimethylallylnaringenin = (–)-(2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3-methylbut-2-enyl)chroman-4-one

Other name(s): N8DT

Systematic name: dimethylallyl-diphosphate:naringenin 8-dimethylallyltransferase

Comments: Requires Mg²⁺. This membrane-bound protein is located in the plastids [2]. In addition to naringenin, the enzyme can prenylate several other flavanones at the C-8 position, but more slowly. Along with EC 1.14.13.103 (8-dimethylallylnaringenin 2'-hydroxylase) and EC 2.5.1.71 (leachianone G 2"-dimethylallyltransferase), this enzyme forms part of the sophoraflavanone-G-biosynthesis pathway.

References:

1. Yamamoto, H., Senda, M. and Inoue, K. Flavanone 8-dimethylallyltransferase in Sophora flavescens cell suspension cultures. Phytochemistry 54 (2000) 649-655. [PMID: 10975499]

2. Zhao, P., Inoue, K., Kouno, I. and Yamamoto, H. Characterization of leachianone G 2"-dimethylallyltransferase, a novel prenyl side-chain elongation enzyme for the formation of the lavandulyl group of sophoraflavanone G in Sophora flavescens Ait. cell suspension cultures. Plant Physiol. 133 (2003) 1306-1313. [PMID: 14551337]

EC 2.5.1.71

Accepted name: leachianone-G 2"-dimethylallyltransferase

Reaction: dimethylallyl diphosphate + leachianone G = diphosphate + sophoraflavanone G

For diagram of reaction, click here

Glossary: leachianone G = (–)-(2S)-2′-hydroxy-8-dimethylallylnaringenin = (–)-(2S)-5,7-dihydroxy-8-(2-hydroxy-3-methylbut-2-enyl)-2-(4-hydroxyphenyl)chroman-4-one
sophoraflavanone G = 2-{[(2S)-2-(2,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-chroman-8-yl]methyl}-5-methyl-hex-4-enoic acid

Other name(s): LG 2"-dimethylallyltransferase; leachianone G 2"-dimethylallyltransferase; LGDT

Systematic name: dimethylallyl-diphosphate:leachianone-G 2"-dimethylallyltransferase

Comments: This membrane-bound enzyme is located in the plastids and requires Mg²⁺ for activity. The reaction forms the lavandulyl sidechain of sophoraflavanone G by transferring a dimethylallyl group to the 2" position of another dimethylallyl group attached at postiion 8 of leachianone G. The enzyme is specific for dimethylallyl diphosphate as the prenyl donor, as it cannot be replaced by isopentenyl diphosphate or geranyl diphosphate. Euchrenone a₇ (a 5-deoxy derivative of leachianone G) and kenusanone I (a 7-methoxy derivative of leachianone G) can also act as substrates, but more slowly. Along with EC 1.14.13.103 (8-dimethylallylnaringenin 2'-hydroxylase) and EC 2.5.1.70 (naringenin 8-dimethylallyltransferase), this enzyme forms part of the sophoraflavanone-G biosynthesis pathway.

References:

1. Zhao, P., Inoue, K., Kouno, I. and Yamamoto, H. Characterization of leachianone G 2"-dimethylallyltransferase, a novel prenyl side-chain elongation enzyme for the formation of the lavandulyl group of sophoraflavanone G in Sophora flavescens Ait. cell suspension cultures. Plant Physiol. 133 (2003) 1306-1313. [PMID: 14551337]

EC 2.6.1.84

Accepted name: arginine—pyruvate transaminase

Reaction: L-arginine + pyruvate = 5-guanidino-2-oxopentanoate + L-alanine

Glossary: 2-ketoarginine = 5-guanidino-2-oxopentanoic acid

Other name(s): arginine:pyruvate transaminase; AruH

Systematic name: L-arginine:pyruvate aminotransferase

Comments: A pyridoxal-phosphate protein. While L-arginine is the best substrate, the enzyme exhibits broad substrate specificity, with L-lysine, L-methionine, L-leucine, ornithine and L-glutamine also able to act as substrates, but more slowly. Pyruvate cannot be replaced by 2-oxoglutarate as amino-group acceptor. This is the first catalytic enzyme of the arginine transaminase pathway for L-arginine utilization in Pseudomonas aeruginosa. This pathway is only used when the major route of arginine catabolism, i.e. the arginine succinyltransferase pathway, is blocked.

References:

1. Yang, Z. and Lu, C.-D. Characterization of an arginine:pyruvate transaminase in arginine catabolism of Pseudomonas aeruginosa PAO1. J. Bacteriol. 189 (2007) 3954-3959. [PMID: 17416668]

2. Yang, Z. and Lu, C.D. Functional genomics enables identification of genes of the arginine transaminase pathway in Pseudomonas aeruginosa. J. Bacteriol. 189 (2007) 3945-3953. [PMID: 17416670]

EC 2.6.1.85

Accepted name: aminodeoxychorismate synthase

Reaction: chorismate + L-glutamine = 4-amino-4-deoxychorismate + L-glutamate

For diagram click here.

Other name(s): ADC synthase; 4-amino-4-deoxychorismate synthase; PabB; chorismate:L-glutamine amido-ligase (incorrect)

Systematic name: chorismate:L-glutamine aminotransferase

Comments: The enzyme is composed of two parts, PabA and PabB. In the absence of PabA and glutamine, PabB converts ammonia and chorismate into 4-amino-4-deoxychorismate (in the presence of Mg²⁺). PabA converts glutamine into glutamate only in the presence of stoichiometric amounts of PabB. This enzyme is coupled with EC 4.1.3.38, aminodeoxychorismate lyase, to form 4-aminobenzoate.

References:

1. Ye, Q.Z., Liu, J. and Walsh, C.T. p-Aminobenzoate synthesis in Escherichia coli: purification and characterization of PabB as aminodeoxychorismate synthase and enzyme X as aminodeoxychorismate lyase. Proc. Natl. Acad. Sci. USA 87 (1990) 9391-9395. [PMID: 2251281]

2. Viswanathan, V.K., Green, J.M. and Nichols, B.P. Kinetic characterization of 4-amino 4-deoxychorismate synthase from Escherichia coli. J. Bacteriol. 177 (1995) 5918-5923. [PMID: 7592344]

[EC 2.7.1.155 Transferred entry: diphosphoinositol-pentakisphosphate kinase. Now EC 2.7.4.24, diphosphoinositol-pentakisphosphate kinase. The enzyme had been incorrectly classified as the reaction involves transfer of a phospho group to another phospho group (EC 2.7.4) rather than to an hydroxy group (EC 2.7.1). (EC 2.7.1.155 created 2003, deleted 2007)]

*EC 2.7.1.26

Accepted name: riboflavin kinase

Reaction: ATP + riboflavin = ADP + FMN

Other name(s): flavokinase; FK; RFK

Systematic name: ATP:riboflavin 5'-phosphotransferase

Comments: The cofactors FMN and FAD participate in numerous processes in all organisms, including mitochondrial electron transport, photosynthesis, fatty-acid oxidation, and metabolism of vitamin B₆, vitamin B₁₂ and folates [5]. While monofunctional riboflavin kinase is found in eukaryotes, some bacteria have a bifunctional enzyme that exhibits both this activity and that of EC 2.7.7.2, FMN adenylyltransferase [5]. A divalent metal cation is required for activity (with different species preffering Mg²⁺, Mn²⁺ or Zn²⁺). In Bacillus subtilis, ATP can be replaced by other phosphate donors but with decreasing enzyme activity in the order ATP > dATP > CTP > UTP [6].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, PDB, CAS registry number: 9032-82-0

References:

1. Chassy, B.M., Arsenis, C. and McCormick, D.B. The effect of the length of the side chain of flavins on reactivity with flavokinase. J. Biol. Chem. 240 (1965) 1338-1340. [PMID: 14284745]

2. Giri, K.V., Krishnaswamy, P.R. and Rao, N.A. Studies on plant flavokinase. Biochem. J. 70 (1958) 66-71. [PMID: 13584303]

3. Kearney, E.B. The interaction of yeast flavokinase with riboflavin analogues. J. Biol. Chem. 194 (1952) 747-754. [PMID: 14927668]

4. McCormick, D.B. and Butler, R.C. Substrate specificity of liver flavokinase. Biochim. Biophys. Acta 65 (1962) 326-332.

5. Sandoval, F.J. and Roje, S. An FMN hydrolase is fused to a riboflavin kinase homolog in plants. J. Biol. Chem. 280 (2005) 38337-38345. [PMID: 16183635]

6. Solovieva, I.M., Tarasov, K.V. and Perumov, D.A. Main physicochemical features of monofunctional flavokinase from Bacillus subtilis. Biochemistry (Mosc) 68 (2003) 177-181. [PMID: 12693963]

7. Solovieva, I.M., Kreneva, R.A., Leak, D.J. and Perumov, D.A. The ribR gene encodes a monofunctional riboflavin kinase which is involved in regulation of the Bacillus subtilis riboflavin operon. Microbiology 145 (1999) 67-73. [PMID: 10206712]

EC 2.7.4.24

Accepted name: diphosphoinositol-pentakisphosphate kinase

Reaction: ATP + 1D-myo-inositol 5-diphosphate pentakisphosphate = ADP + 1D-myo-inositol bisdiphosphate tetrakisphosphate (isomeric configuration unknown)

Glossary: PP-InsP₅ = 1D-myo-inositol 5-diphosphate pentakisphosphate
PP-InsP₄-PP = 1D-myo-inositol bisdiphosphate tetrakisphosphate

Other name(s): PP-IP₅ kinase; diphosphoinositol pentakisphosphate kinase; ATP:5-diphospho-1D-myo-inositol-pentakisphosphate phosphotransferase

Systematic name: ATP:1D-myo-inositol-5-diphosphate-pentakisphosphate phosphotransferase

References:

1. Shears, S.B., Ali, N., Craxton, A. and Bembenek, M.E. Synthesis and metabolism of bis-diphosphoinositol tetrakisphosphate in vitro and in vivo. J. Biol. Chem. 270 (1995) 10489-10497. [PMID: 7737983]

2. Albert, C., Safrany, S.T., Bembenek, M.E., Reddy, K.M., Reddy, K.K., Falck, J.-R., Bröcker, M., Shears, S.B. and Mayr, G.W. Biological variability in the structures of diphosphoinositol polyphosphates in Dictyostelium discoideum and mammalian cells. Biochem. J. 327 (1997) 553-560. [PMID: 9359429]

*EC 2.7.7.2

Accepted name: FAD synthetase

Reaction: ATP + FMN = diphosphate + FAD

Other name(s): FAD pyrophosphorylase; riboflavin mononucleotide adenylyltransferase; adenosine triphosphate-riboflavin mononucleotide transadenylase; adenosine triphosphate-riboflavine mononucleotide transadenylase; riboflavin adenine dinucleotide pyrophosphorylase; riboflavine adenine dinucleotide adenylyltransferase; flavin adenine dinucleotide synthetase; FADS; FMN adenylyltransferase

Systematic name: ATP:FMN adenylyltransferase

Comments: Requires Mg²⁺ and is highly specific for ATP as phosphate donor [5]. The cofactors FMN and FAD participate in numerous processes in all organisms, including mitochondrial electron transport, photosynthesis, fatty-acid oxidation, and metabolism of vitamin B₆, vitamin B₁₂ and folates [3]. While monofunctional FAD synthetase is found in eukaryotes and in some prokaryotes, most prokaryotes have a bifunctional enzyme that exhibits both this activity and that of EC 2.7.1.26, riboflavin kinase [3,5].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, CAS registry number: 9026-37-3

References:

1. Giri, K.V., Rao, N.A., Cama, H.R. and Kumar, S.A. Studies on flavinadenine dinucleotide-synthesizing enzyme in plants. Biochem. J. 75 (1960) 381-386. [PMID: 13828163]

2. Schrecker, A.W. and Kornberg, A. Reversible enzymatic synthesis of flavin-adenine dinucleotide. J. Biol. Chem. 182 (1950) 795-803.

3. Sandoval, F.J. and Roje, S. An FMN hydrolase is fused to a riboflavin kinase homolog in plants. J. Biol. Chem. 280 (2005) 38337-38345. [PMID: 16183635]

4. Oka, M. and McCormick, D.B. Complete purification and general characterization of FAD synthetase from rat liver. J. Biol. Chem. 262 (1987) 7418-7422. [PMID: 3034893]

5. Brizio, C., Galluccio, M., Wait, R., Torchetti, E.M., Bafunno, V., Accardi, R., Gianazza, E., Indiveri, C. and Barile, M. Over-expression in Escherichia coli and characterization of two recombinant isoforms of human FAD synthetase. Biochem. Biophys. Res. Commun. 344 (2006) 1008-1016. [PMID: 16643857]

*EC 3.1.1.14

Accepted name: chlorophyllase

Reaction: chlorophyll + H₂O = phytol + chlorophyllide

For diagram click here

Other name(s): CLH; Chlase

Systematic name: chlorophyll chlorophyllidohydrolase

Comments: Chlorophyllase has been found in higher plants, diatoms, and in the green algae Chlorella [3]. This enzyme forms part of the chlorophyll degradation pathway and is thought to take part in de-greening processes such as fruit ripening, leaf senescence and flowering, as well as in the turnover and homeostasis of chlorophyll [4]. This enzyme acts preferentially on chlorophyll a but will also accept chlorophyll b and pheophytins as substrates [5]. Ethylene and methyl jasmonate, which are known to accelerate senescence in many species, can enhance the activity of the hormone-inducible form of this enzyme [5].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, CAS registry number: 9025-96-1

References:

1. Holden, M. The breakdown of chlorophyll by chlorophyllase. Biochem. J. 78 (1961) 359-364. [PMID: 13715233]

2. Klein, A.O. and Vishniac, W. Activity and partial purification of chlorophyllase in aqueous systems. J. Biol. Chem. 236 (1961) 2544-2547. [PMID: 13756631]

3. Tsuchiya, T., Ohta, H., Okawa, K., Iwamatsu, A., Shimada, H., Masuda, T. and Takamiya, K. Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: finding of a lipase motif and the induction by methyl jasmonate. Proc. Natl. Acad. Sci. USA 96 (1999) 15362-15367. [PMID: 10611389]

4. Okazawa, A., Tango, L., Itoh, Y., Fukusaki, E. and Kobayashi, A. Characterization and subcellular localization of chlorophyllase from Ginkgo biloba. Z. Naturforsch. [C] 61 (2006) 111-117. [PMID: 16610227]

5. Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55-77. [PMID: 16669755]

EC 3.1.1.81

Accepted name: quorum-quenching N-acyl-homoserine lactonase

Reaction: an N-acyl-L-homoserine lactone + H₂O = an N-acyl-L-homoserine

Other name(s): acyl homoserine degrading enzyme; acyl-homoserine lactone acylase; AHL lactonase; AHL-degrading enzyme; AHL-inactivating enzyme; AHLase; AhlD; AhlK; AiiA; AiiA lactonase; AiiA-like protein; AiiB; AiiC; AttM; delactonase; lactonase-like enzyme; N-acyl homoserine lactonase; N-acyl homoserine lactone hydrolase; N-acyl-homoserine lactone lactonase; N-acyl-L-homoserine lactone hydrolase; PvdQ; QuiP; quorum-quenching lactonase; quorum-quenching N-acyl homoserine lactone hydrolase

Systematic name: N-acyl-L-homoserine-lactone lactonohydrolase

Comments: Acyl-homoserine lactones (AHLs) are produced by a number of bacterial species and are used by them to regulate the expression of virulence genes in a process known as quorum-sensing. Each bacterial cell has a basal level of AHL and, once the population density reaches a critical level, it triggers AHL-signalling which, in turn, initiates the expression of particular virulence genes [5]. Plants or animals capable of degrading AHLs would have a therapeutic advantage in avoiding bacterial infection as they could prevent AHL-signalling and the expression of virulence genes in quorum-sensing bacteria [5]. N-(3-Oxohexanoyl)-L-homoserine lactone, N-(3-oxododecanoyl)-L-homoserine lactone, N-butanoyl-L-homoserine lactone and N-(3-oxooctanoyl)-L-homoserine lactone can act as substrates [5].

References:

1. Thomas, P.W., Stone, E.M., Costello, A.L., Tierney, D.L. and Fast, W. The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein. Biochemistry 44 (2005) 7559-7569. [PMID: 15895999]

2. Dong, Y.H., Gusti, A.R., Zhang, Q., Xu, J.L. and Zhang, L.H. Identification of quorum-quenching N-acyl homoserine lactonases from Bacillus species. Appl. Environ. Microbiol. 68 (2002) 1754-1759. [PMID: 11916693]

3. Wang, L.H., Weng, L.X., Dong, Y.H. and Zhang, L.H. Specificity and enzyme kinetics of the quorum-quenching N-acyl homoserine lactone lactonase (AHL-lactonase). J. Biol. Chem. 279 (2004) 13645-13651. [PMID: 14734559]

4. Dong, Y.H., Xu, J.L., Li, X.Z. and Zhang, L.H. AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc. Natl. Acad. Sci. USA 97 (2000) 3526-3531. [PMID: 10716724]

5. Dong, Y.H., Wang, L.H., Xu, J.L., Zhang, H.B., Zhang, X.F. and Zhang, L.H. Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature 411 (2001) 813-817. [PMID: 11459062]

6. Lee, S.J., Park, S.Y., Lee, J.J., Yum, D.Y., Koo, B.T. and Lee, J.K. Genes encoding the N-acyl homoserine lactone-degrading enzyme are widespread in many subspecies of Bacillus thuringiensis. Appl. Environ. Microbiol. 68 (2002) 3919-3924. [PMID: 12147491]

7. Park, S.Y., Lee, S.J., Oh, T.K., Oh, J.W., Koo, B.T., Yum, D.Y. and Lee, J.K. AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria. Microbiology 149 (2003) 1541-1550. [PMID: 12777494]

8. Ulrich, R.L. Quorum quenching: enzymatic disruption of N-acylhomoserine lactone-mediated bacterial communication in Burkholderia thailandensis. Appl. Environ. Microbiol. 70 (2004) 6173-6180. [PMID: 15466564]

9. Kim, M.H., Choi, W.C., Kang, H.O., Lee, J.S., Kang, B.S., Kim, K.J., Derewenda, Z.S., Oh, T.K., Lee, C.H. and Lee, J.K. The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase. Proc. Natl. Acad. Sci. USA 102 (2005) 17606-17611. [PMID: 16314577]

10. Liu, D., Lepore, B.W., Petsko, G.A., Thomas, P.W., Stone, E.M., Fast, W. and Ringe, D. Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis. Proc. Natl. Acad. Sci. USA 102 (2005) 11882-11887. [PMID: 16087890]

11. Yang, F., Wang, L.H., Wang, J., Dong, Y.H., Hu, J.Y. and Zhang, L.H. Quorum quenching enzyme activity is widely conserved in the sera of mammalian species. FEBS Lett. 579 (2005) 3713-3717. [PMID: 15963993]

EC 3.1.1.82

Accepted name: pheophorbidase

Reaction: pheophorbide a + H₂O = pyropheophorbide a + methanol + CO₂ (overall reaction)
(1a) pheophorbide a + H₂O = C-13²-carboxypyropheophorbide a + methanol
(1b) C-13²-carboxypyropheophorbide a = pyropheophorbide a + CO₂ (spontaneous)

For diagram click here

Other name(s): phedase; PPD

Systematic name: pheophorbide-a hydrolase

Comments: This enzyme forms part of the chlorophyll degradation pathway, and is found in higher plants and in algae. In higher plants it participates in de-greening processes such as fruit ripening, leaf senescence, and flowering. The enzyme exists in two forms: type 1 is induced by senescence whereas type 2 is constitutively expressed [1,2]. The enzyme is highly specific for pheophorbide as substrate (with a preference for pheophorbide a over pheophorbide b) as other chlorophyll derivatives such as protochlorophyllide a, pheophytin a and c, chlorophyll a and b, and chlorophyllide a cannot act as substrates [2]. Another enzyme, called pheophorbide demethoxycarbonylase (PDC), produces pyropheophorbide a from pheophorbide a without forming an intermediate although the precise reaction is not yet known [1].

References:

1. Suzuki, Y., Doi, M. and Shioi, Y. Two enzymatic reaction pathways in the formation of pyropheophorbide a. Photosynth. Res. 74 (2002) 225-233. [PMID: 16228561]

2. Suzuki, Y., Amano, T. and Shioi, Y. Characterization and cloning of the chlorophyll-degrading enzyme pheophorbidase from cotyledons of radish. Plant Physiol. 140 (2006) 716-725. [PMID: 16384908]

3. Hörtensteiner, S. Chlorophyll degradation during senescence. Annu. Rev. Plant Biol. 57 (2006) 55-77. [PMID: 16669755]

EC 3.2.1.163

Accepted name: 1,6-α-D-mannosidase

Reaction: Hydrolysis of the 1,6-linked α-D-mannose residues in α-D-Manp-(1→6)-D-Manp

Systematic name: 1,6-α-mannosyl α-D-mannohydrolase

Comments: The enzyme is specific for (1→6)-linked mannobiose and has no activity towards any other linkages, or towards p-nitrophenyl-α-D-mannopyranoside or baker's yeast mannan. It is strongly inhibited by Mn²⁺ but does not require Ca²⁺ or any other metal cofactor for activity.

References:

1. Athanasopoulos, V.I., Niranjan, K. and Rastall, R.A. The production, purification and characterisation of two novel α-D-mannosidases from Aspergillus phoenicis. Carbohydr. Res. 340 (2005) 609-617. [PMID: 15721331]

EC 3.2.1.164

Accepted name: galactan endo-1,6-β-galactosidase

Reaction: Endohydrolysis of 1,6-β-D-galactosidic linkages in arabinogalactan proteins and 1,3:1,6-β-galactans to yield galactose and β-(1→6)-galactaobiose as the final products

Other name(s): endo-1,6-β-galactanase; endo-β-(1→6)-galactanase

Comments: The enzyme specifically hydrolyses 1,6-β-D-galactooligosaccharides with a degree of polymerization (DP) higher than 3, and their acidic derivatives with 4-O-methylglucosyluronate or glucosyluronate groups at the non-reducing terminals [2]. 1,3-β-D- and 1,4-β-D-galactosyl residues cannot act as substrates. The enzyme can also hydrolyse α-L-arabinofuranosidase-treated arabinogalactan protein (AGP) extracted from radish roots [2,3]. AGPs are thought to be involved in many physiological events, such as cell division, cell expansion and cell death [3].

References:

1. Brillouet, J.-M., Williams, P. and Moutounet, M. Purification and some properties of a novel endo-β-(1→6)-D-galactanase from Aspergillus niger. Agric. Biol. Chem. 55 (1991) 1565-1571.

2. Okemoto, K., Uekita, T., Tsumuraya, Y., Hashimoto, Y. and Kasama, T. Purification and characterization of an endo-β-(1→6)-galactanase from Trichoderma viride. Carbohydr. Res. 338 (2003) 219-230. [PMID: 12543554]

3. Kotake, T., Kaneko, S., Kubomoto, A., Haque, M.A., Kobayashi, H. and Tsumuraya, Y. Molecular cloning and expression in Escherichia coli of a Trichoderma viride endo-β-(1→6)-galactanase gene. Biochem. J. 377 (2004) 749-755. [PMID: 14565843]

EC 3.4.15.6

Accepted name: cyanophycinase

Reaction: [L-Asp(4-L-Arg)]_n + H₂O = [L-Asp(4-L-Arg)]_n-1 + L-Asp(4-L-Arg)

For diagram click here.

Glossary: cyanophycin = [L-Asp(4-L-Arg)]_n = N-β-aspartylarginine = [L-4-(L-arginin-2-N-yl)aspartic acid]_n = poly{N⁴-[(1S)-1-carboxy-4-guanidinobutyl]-L-asparagine}

Other name(s): cyanophycin degrading enzyme; β-Asp-Arg hydrolysing enzyme; CGPase; CphB; CphE; cyanophycin granule polypeptidase; extracellular CGPase

Comments: The enzyme is highly specific for the branched polypeptide cyanophycin and does not hydrolyse poly-L-aspartate or poly-L-arginine [3]. A serine-type exopeptidase that belongs in peptidase family S51.

References:

1. Obst, M., Krug, A., Luftmann, H. and Steinbüchel, A. Degradation of cyanophycin by Sedimentibacter hongkongensis strain KI and Citrobacter amalonaticus strain G isolated from an anaerobic bacterial consortium. Appl. Environ. Microbiol. 71 (2005) 3642-3652. [PMID: 16000772]

2. Obst, M., Oppermann-Sanio, F.B., Luftmann, H. and Steinbüchel, A. Isolation of cyanophycin-degrading bacteria, cloning and characterization of an extracellular cyanophycinase gene (cphE) from Pseudomonas anguilliseptica strain BI. The cphE gene from P. anguilliseptica BI encodes a cyanophycin-hydrolyzing enzyme. J. Biol. Chem. 277 (2002) 25096-25105. [PMID: 11986309]

3. Richter, R., Hejazi, M., Kraft, R., Ziegler, K. and Lockau, W. Cyanophycinase, a peptidase degrading the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartic acid (cyanophycin): molecular cloning of the gene of Synechocystis sp. PCC 6803, expression in Escherichia coli, and biochemical characterization of the purified enzyme. Eur. J. Biochem. 263 (1999) 163-169. [PMID: 10429200]

EC 3.4.22.65

Accepted name: peptidase 1 (mite)

Reaction: Broad endopeptidase specificity

Other name(s): allergen Der f 1; allergen Der p 1; antigen Der p 1; antigen Eur m 1; antigen Pso o 1; major mite fecal allergen Der p 1; Der p 1; Der f 1; Eur m 1; endopeptidase 1 (mite)

Comments: This enzyme, derived from the house dust mite, is a major component of the allergic immune response [2]. The substrate specificity of this enzyme is not altogether clear. It cleaves the low-affinity IgE receptor CD23 at Glu²⁹⁸Ser²⁹⁹ and Ser¹⁵⁵Ser¹⁵⁶ [1]. It also cleaves the pulmonary structural proteins occludin and claudin at LeuLeu, AspLeu and at GlyThr bonds [1,2]. It can also cleave the α subunit of the interleukin-2 (IL-2) receptor (CD25) [4]. Using a positional scanning combinatorial library, it was found that the major substrate-specificity determinant is for Ala in the P2 position [3]. The enzyme shows only a slight preference for basic amino acids in the P1 and P3 positions and a preference for aliphatic amino acids such as Ile, Pro, Val, Leu and norleucine in the P4 position [3]. Belongs in peptidase family C1A.

References:

1. Meighan, P. and Pirzad, R. Mite endopeptidase 1. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Eds), Handbook of Proteolytic Enzymes, 2nd edn, Elsevier, London, 2004, pp. 1187-1189.

2. Kalsheker, N.A., Deam, S., Chambers, L., Sreedharan, S., Brocklehurst, K. and Lomas, D.A. The house dust mite allergen Der p1 catalytically inactivates α1-antitrypsin by specific reactive centre loop cleavage: a mechanism that promotes airway inflammation and asthma. Biochem. Biophys. Res. Commun. 221 (1996) 59-61. [PMID: 8660343]

3. Harris, J., Mason, D.E., Li, J., Burdick, K.W., Backes, B.J., Chen, T., Shipway, A., Van Heeke, G., Gough, L., Ghaemmaghami, A., Shakib, F., Debaene, F. and Winssinger, N. Activity profile of dust mite allergen extract using substrate libraries and functional proteomic microarrays. Chem. Biol. 11 (2004) 1361-1372. [PMID: 15489163]

4. Schulz, O., Sewell, H.F. and Shakib, F. Proteolytic cleavage of CD25, the α subunit of the human T cell interleukin 2 receptor, by Der p 1, a major mite allergen with cysteine protease activity. J. Exp. Med. 187 (1998) 271-275. [PMID: 9432986]

5. Schulz, O., Sewell, H.F. and Shakib, F. A sensitive fluorescent assay for measuring the cysteine protease activity of Der p 1, a major allergen from the dust mite Dermatophagoides pteronyssinus. Mol. Pathol. 51 (1998) 222-224. [PMID: 9893750]

6. Takai, T., Kato, T., Sakata, Y., Yasueda, H., Izuhara, K., Okumura, K. and Ogawa, H. Recombinant Der p 1 and Der f 1 exhibit cysteine protease activity but no serine protease activity. Biochem. Biophys. Res. Commun. 328 (2005) 944-952. [PMID: 15707969]

EC 3.4.22.66

Accepted name: calicivirin

Reaction: Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu and the P1' position is occupied by Gly

Other name(s): Camberwell virus processing peptidase; Chiba virus processing peptidase; Norwalk virus processing peptidase; Southampton virus processing peptidase; Southampton virus; norovirus virus processing peptidase; calicivirus trypsin-like cysteine protease; calicivirus TCP; calicivirus 3C-like protease; calicivirus endopeptidase; rabbit hemorrhagic disease virus 3C endopeptidase

Comments: Viruses that are members of the Norovirus genus (Caliciviridae family) are a major cause of epidemic acute viral gastroenteritis [4]. The nonstructural proteins of these viruses are produced by proteolytic cleavage of a large precursor polyprotein, performed by a protease that is incorporated into the polyprotein [6]. Cleavage sites are apparently defined by features based on both sequence and structure since several sites in the polyprotein fulfilling the identified sequence requirements are not cleaved [1]. The presence of acidic (Asp), basic (Arg), aromatic (Tyr) or aliphatic (Leu) amino acids at the P1′ position results in only minor differences in cleavage efficiency, suggesting that steric or conformational constraints may play a role in determining specificity [1]. Changes to the amino acid at the P2 position do not alter cleavage efficiency [1,2]. Belongs in peptidase family C37.

References:

1. Meyers, G., Rossi, C. and Thiel, H.J. Calicivirus endopeptidases. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Eds), Handbook of Proteolytic Enzymes, 2nd edn, Elsevier, London, 2004, pp. 1380-1382.

2. Wirblich, C., Sibilia, M., Boniotti, M.B., Rossi, C., Thiel, H.J. and Meyers, G. 3C-like protease of rabbit hemorrhagic disease virus: identification of cleavage sites in the ORF1 polyprotein and analysis of cleavage specificity. J. Virol. 69 (1995) 7159-7168. [PMID: 7474137]

3. Martín Alonso, J.M., Casais, R., Boga, J.A. and Parra, F. Processing of rabbit hemorrhagic disease virus polyprotein. J. Virol. 70 (1996) 1261-1265. [PMID: 8551592]

4. Liu, B., Clarke, I.N. and Lambden, P.R. Polyprotein processing in Southampton virus: identification of 3C-like protease cleavage sites by in vitro mutagenesis. J. Virol. 70 (1996) 2605-2610. [PMID: 8642693]

5. Liu, B.L., Viljoen, G.J., Clarke, I.N. and Lambden, P.R. Identification of further proteolytic cleavage sites in the Southampton calicivirus polyprotein by expression of the viral protease in E. coli. J. Gen. Virol. 80 (1999) 291-296. [PMID: 10073687]

EC 3.4.22.67

Accepted name: zingipain

Reaction: Preferential cleavage of peptides with a proline residue at the P2 position

Other name(s): ginger protease; GP-I; GP-II; ginger protease II (Zingiber officinale); zingibain

Comments: This enzyme is found in ginger (Zingiber officinale) rhizome and is a member of the papain family. GP-II contains two glycosylation sites. The enzyme is inhibited by some divalent metal ions, such as Hg²⁺, Cu²⁺, Cd²⁺ and Zn²⁺ [2]. Belongs in peptidase family C1.

References:

1. Choi, K.H. and Laursen, R.A. Amino-acid sequence and glycan structures of cysteine proteases with proline specificity from ginger rhizome Zingiber officinale. Eur. J. Biochem. 267 (2000) 1516-1526. [PMID: 10691991]

2. Ohtsuki, K., Taguchi, K., Sato, K. and Kawabata, M. Purification of ginger proteases by DEAE-Sepharose and isoelectric focusing. Biochim. Biophys. Acta 1243 (1995) 181-184. [PMID: 7873561]

3. Choi, K.H., Laursen, R.A. and Allen, K.N. The 2.1 Å structure of a cysteine protease with proline specificity from ginger rhizome, Zingiber officinale. Biochemistry 38 (1999) 11624-11633. [PMID: 10512617]

EC 3.5.1.97

Accepted name: acyl-homoserine-lactone acylase

Reaction: an N-acyl-L-homoserine lactone + H₂O = L-homoserine lactone + a carboxylate

Other name(s): acyl-homoserine lactone acylase; AHL-acylase; AiiD; N-acyl-homoserine lactone acylase; PA2385 protein; quorum-quenching AHL acylase; quorum-quenching enzyme

Systematic name: N-acyl-L-homoserine-lactone amidohydrolase

Comments: Acyl-homoserine lactones (AHLs) are produced by a number of bacterial species and are used by them to regulate the expression of virulence genes in a process known as quorum-sensing. Each bacterial cell has a basal level of AHL and, once the population density reaches a critical level, it triggers AHL-signalling which, in turn, initiates the expression of particular virulence genes. Plants or animals capable of degrading AHLs would have a therapeutic advantage in avoiding bacterial infection as they could prevent AHL-signalling and the expression of virulence genes in quorum-sensing bacteria. This quorum-quenching enzyme removes the fatty-acid side chain from the homoserine lactone ring of AHL-dependent quorum-sensing signal molecules [1]. It has broad specificity for AHLs with side changes ranging in length from 11 to 14 carbons. Substituents at the 3'-position, as found in N-(3-oxododecanoyl)-L-homoserine lactone, do not affect this activity [1].

References:

1. Sio, C.F., Otten, L.G., Cool, R.H., Diggle, S.P., Braun, P.G., Bos, R., Daykin, M., Cámara, M., Williams, P. and Quax, W.J. Quorum quenching by an N-acyl-homoserine lactone acylase from Pseudomonas aeruginosa PAO1. Infect. Immun. 74 (2006) 1673-1682. [PMID: 16495538]

2. Lin, Y.H., Xu, J.L., Hu, J., Wang, L.H., Ong, S.L., Leadbetter, J.R. and Zhang, L.H. Acyl-homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum-quenching enzymes. Mol. Microbiol. 47 (2003) 849-860. [PMID: 12535081]

*EC 4.1.2.37

Accepted name: hydroxynitrilase

Reaction: acetone cyanohydrin = cyanide + acetone

Glossary: acetone cyanohydrin = 2-hydroxyisobutyronitrile

Other name(s): α-hydroxynitrile lyase; hydroxynitrile lyase; acetone-cyanhydrin lyase [mis-spelt]; acetone-cyanohydrin acetone-lyase; oxynitrilase; 2-hydroxyisobutyronitrile acetone-lyase; 2-hydroxyisobutyronitrile acetone-lyase (cyanide-forming); acetone-cyanohydrin lyase

Systematic name: acetone-cyanohydrin acetone-lyase (cyanide-forming)

Comments: This enzyme accepts aliphatic and aromatic hydroxynitriles, unlike EC 4.1.2.11 (hydroxymandelonitrile lyase) which does not act on aliphatic hydroxynitriles. 2-Hydroxyisobutyronitrile (acetone cyanohydrin) is liberated by glycosidase action on linamarin.

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, CAS registry number: 112567-89-2

References:

1. Xu, L.-L., Singh, B.K. and Conn, E.E. Purification and characterization of acetone cyanohydrin lyase from Linum usitatissimum. Arch. Biochem. Biophys. 263 (1988) 256-263. [PMID: 3377504]

2. Selmar, D., Lieberei, R., Biehl, B., Conn, E.E. α-Hydroxynitrile lyase in Hevea brasiliensis and its significance for rapid cyanogenesis. Physiol. Plant 75 (1989) 97-101.

[EC 4.1.2.39 Deleted entry: hydroxynitrilase. The enzyme is identical to EC 4.1.2.37, hydroxynitrilase. (EC 4.1.2.39 created 1999, deleted 2007)]

EC 4.1.2.42

Accepted name: D-threonine aldolase

Reaction: (1) D-threonine = glycine + acetaldehyde
(2) D-allothreonine = glycine + acetaldehyde

Glossary: D-threonine = (2R,3S)-2-amino-3-hydroxybutanoic acid
D-allothreonine = (2R,3R)-2-amino-3-hydroxybutanoic acid

Other name(s): D-TA; DTA; low specificity D-TA; low specificity D-threonine aldolase

Systematic name: D-threonine acetaldehyde-lyase (glycine-forming)

Comments: A pyridoxal-phosphate protein that is activated by divalent metal cations (e.g. Co²⁺, Ni²⁺, Mn²⁺ or Mg²⁺) [1,2]. The reaction is reversible, which can lead to the interconversion of D-threonine and D-allothreonine [1]. Several other D-β-hydroxy-α-amino acids, such as D-β-phenylserine, D-β-hydroxy-α-aminovaleric acid and D-β-3,4-dihydroxyphenylserine, can also act as substrate [1].

References:

1. Kataoka, M., Ikemi, M., Morikawa, T., Miyoshi, T., Nishi, K., Wada, M., Yamada, H. and Shimizu, S. Isolation and characterization of D-threonine aldolase, a pyridoxal-5'-phosphate-dependent enzyme from Arthrobacter sp. DK-38. Eur. J. Biochem. 248 (1997) 385-393. [PMID: 9346293]

2. Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. A novel metal-activated pyridoxal enzyme with a unique primary structure, low specificity D-threonine aldolase from Arthrobacter sp. Strain DK-38. Molecular cloning and cofactor characterization. J. Biol. Chem. 273 (1998) 16678-16685. [PMID: 9642221]

3. Liu, J.Q., Odani, M., Dairi, T., Itoh, N., Shimizu, S. and Yamada, H. A new route to L-threo-3-[4-(methylthio)phenylserine], a key intermediate for the synthesis of antibiotics: recombinant low-specificity D-threonine aldolase-catalyzed stereospecific resolution. Appl. Microbiol. Biotechnol. 51 (1999) 586-591. [PMID: 10390816]

4. Liu, J.Q., Odani, M., Yasuoka, T., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Gene cloning and overproduction of low-specificity D-threonine aldolase from Alcaligenes xylosoxidans and its application for production of a key intermediate for parkinsonism drug. Appl. Microbiol. Biotechnol. 54 (2000) 44-51. [PMID: 10952004]

5. Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Diversity of microbial threonine aldolases and their application. J. Mol. Catal. B 10 (2000) 107-115.

6. Paiardini, A., Contestabile, R., D'Aguanno, S., Pascarella, S. and Bossa, F. Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B₆-dependent enzymes. Biochim. Biophys. Acta 1647 (2003) 214-219. [PMID: 12686135]

EC 4.1.99.12

Accepted name: 3,4-dihydroxy-2-butanone-4-phosphate synthase

Reaction: D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate

Other name(s): DHBP synthase; L-3,4-dihydroxybutan-2-one-4-phosphate synthase

Systematic name: D-ribulose 5-phosphate formate-lyase (L-3,4-dihydroxybutan-2-one 4-phosphate-forming)

Comments: Requires a divalent cation, preferably Mg²⁺, for activity [1]. The reaction involves an intramolecular skeletal rearrangement, with the bonds in D-ribulose 5-phosphate that connect C-3 and C-5 to C-4 being broken, C-4 being removed as formate and reconnection of C-3 and C-5 [1]. The phosphorylated four-carbon product (L-3,4-dihydroxybutan-2-one 4-phosphate) is an intermediate in the biosynthesis of riboflavin [1].

References:

1. Volk, R. and Bacher, A. Studies on the 4-carbon precursor in the biosynthesis of riboflavin. Purification and properties of L-3,4-dihydroxy-2-butanone-4-phosphate synthase. J. Biol. Chem. 265 (1990) 19479-19485. [PMID: 2246238]

2. Liao, D.I., Calabrese, J.C., Wawrzak, Z., Viitanen, P.V. and Jordan, D.B. Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis. Structure 9 (2001) 11-18. [PMID: 11342130]

3. Kelly, M.J., Ball, L.J., Krieger, C., Yu, Y., Fischer, M., Schiffmann, S., Schmieder, P., Kühne, R., Bermel, W., Bacher, A., Richter, G. and Oschkinat, H. The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase and ligand binding studies reveal the location of the active site. Proc. Natl. Acad. Sci. USA 98 (2001) 13025-13030. [PMID: 11687623]

4. Liao, D.I., Zheng, Y.J., Viitanen, P.V. and Jordan, D.B. Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase. Biochemistry 41 (2002) 1795-1806. [PMID: 11827524]

5. Fischer, M., Römisch, W., Schiffmann, S., Kelly, M., Oschkinat, H., Steinbacher, S., Huber, R., Eisenreich, W., Richter, G. and Bacher, A. Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii. J. Biol. Chem. 277 (2002) 41410-41416. [PMID: 12200440]

6. Steinbacher, S., Schiffmann, S., Richter, G., Huber, R., Bacher, A. and Fischer, M. Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism. J. Biol. Chem. 278 (2003) 42256-42265. [PMID: 12904291]

7. Steinbacher, S., Schiffmann, S., Bacher, A. and Fischer, M. Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1338-1340. [PMID: 15213409]

8. Echt, S., Bauer, S., Steinbacher, S., Huber, R., Bacher, A. and Fischer, M. Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans. J. Mol. Biol. 341 (2004) 1085-1096. [PMID: 15328619]

EC 4.2.1.113

Accepted name: o-succinylbenzoate synthase

Reaction: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H₂O

For diagram click here.

Glossary: 2-succinylbenzoate = o-succinylbenzoate = 4-(2-carboxyphenyl)-4-oxobutanoate

Other name(s): o-succinylbenzoic acid synthase; OSB synthase; OSBS; 2-succinylbenzoate synthase

Systematic name: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate hydrolyase (2-succinylbenzoate-forming)

Comments: Belongs to the enolase superfamily and requires divalent cations, preferably Mg²⁺ or Mn²⁺, for activity. Forms part of the vitamin-K-biosynthesis pathway.

References:

1. Klenchin, V.A., Taylor Ringia, E.A., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli. Biochemistry 42 (2003) 14427-14433. [PMID: 14661953]

2. Palmer, D.R., Garrett, J.B., Sharma, V., Meganathan, R., Babbitt, P.C. and Gerlt, J.A. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry 38 (1999) 4252-4258. [PMID: 10194342]

3. Thompson, T.B., Garrett, J.B., Taylor, E.A., Meganathan, R., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg²⁺ and o-succinylbenzoate. Biochemistry 39 (2000) 10662-10676. [PMID: 10978150]

4. Taylor Ringia, E.A., Garrett, J.B., Thoden, J.B., Holden, H.M., Rayment, I. and Gerlt, J.A. Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry 43 (2004) 224-229. [PMID: 14705949]

EC 4.2.2.22

Accepted name: pectate trisaccharide-lyase

Reaction: eliminative cleavage of unsaturated trigalacturonate as the major product from the reducing end of polygalacturonic acid/pectate

Other name(s): exopectate-lyase; pectate lyase A; PelA

Systematic name: (1→4)-α-D-galacturonan reducing-end-trisaccharide-lyase

Comments: Differs in specificity from EC 4.2.2.9, pectate disaccharide-lyase, as the predominant action is removal of a trisaccharide rather than a disaccharide from the reducing end. Disaccharides and tetrasaccharides may also be removed [2].

References:

1. Kluskens, L.D., van Alebeek, G.J., Voragen, A.G., de Vos, W.M. and van der Oost, J. Molecular and biochemical characterization of the thermoactive family 1 pectate lyase from the hyperthermophilic bacterium Thermotoga maritima. Biochem. J. 370 (2003) 651-659. [PMID: 12443532]

2. Tamaru, Y. and Doi, R.H. Pectate lyase A, an enzymatic subunit of the Clostridium cellulovorans cellulosome. Proc. Natl. Acad. Sci. USA 98 (2001) 4125-4129. [PMID: 11259664]

3. Berensmeier, S., Singh, S.A., Meens, J. and Buchholz, K. Cloning of the pelA gene from Bacillus licheniformis 14A and biochemical characterization of recombinant, thermostable, high-alkaline pectate lyase. Appl. Microbiol. Biotechnol. 64 (2004) 560-567. [PMID: 14673544]

[EC 4.3.1.11 Deleted entry: dihydroxyphenylalanine ammonia-lyase. The entry had been drafted on the basis of a single abstract that did not provide experimental evidence of the enzyme-catalysed reaction. (EC 4.3.1.11 created 1972, deleted 2007)]

EC 4.3.1.22

Accepted name: 3,4-dihydroxyphenylalanine reductive deaminase

Reaction: 3,4-dihydroxy-L-phenylalanine + 2 NADH = 3,4-dihydroxyphenylpropanoate + 2 NAD⁺ + NH₃

Glossary: DOPA = L-dopa = 3,4-dihydroxy-L-phenylalanine

Other name(s): reductive deaminase; DOPA-reductive deaminase; DOPARDA

Systematic name: 3,4-dihydroxy-L-phenylalanine ammonia-lyase (3,4-dihydroxyphenylpropanoate-forming)

Comments: Forms part of the L-phenylalanine-catabolism pathway in the anoxygenic phototrophic bacterium Rhodobacter sphaeroides OU5. NADPH is oxidized more slowly than NADH.

References:

1. Ranjith, N.K., Sasikala, Ch. and Ramana, Ch.V. Catabolism of L-phenylalanine and L-tyrosine by Rhodobacter sphaeroides OU5 occurs through 3,4-dihydroxyphenylalanine. Res. Microbiol. 158 (2007) 506-511. [PMID: 17616348]

EC 5.1.1.18

Accepted name: serine racemase

Reaction: L-serine = D-serine

Other name(s): SRR

Systematic name: serine racemase

Comments: A pyridoxal-phosphate protein that is highly selective for L-serine as substrate. D-Serine is found in type-II astrocytes in mammalian brain, where it appears to be an endogenous ligand of the glycine site of N-methyl-D-aspartate (NMDA) receptors [1,2]. The reaction can also occur in the reverse direction but does so more showly at physiological serine concentrations [4].

References:

1. Wolosker, H., Blackshaw, S. and Snyder, S.H. Serine racemase: a glial enzyme synthesizing D-serine to regulate glutamate-N-methyl-D-aspartate neurotransmission. Proc. Natl. Acad. Sci. USA 96 (1999) 13409-13414. [PMID: 10557334]

2. Wolosker, H., Sheth, K.N., Takahashi, M., Mothet, J.P., Brady, R.O., Jr., Ferris, C.D. and Snyder, S.H. Purification of serine racemase: biosynthesis of the neuromodulator D-serine. Proc. Natl. Acad. Sci. USA 96 (1999) 721-725. [PMID: 9892700]

3. De Miranda, J., Santoro, A., Engelender, S. and Wolosker, H. Human serine racemase: moleular cloning, genomic organization and functional analysis. Gene 256 (2000) 183-188. [PMID: 11054547]

4. Foltyn, V.N., Bendikov, I., De Miranda, J., Panizzutti, R., Dumin, E., Shleper, M., Li, P., Toney, M.D., Kartvelishvily, E. and Wolosker, H. Serine racemase modulates intracellular D-serine levels through an α,β-elimination activity. J. Biol. Chem. 280 (2005) 1754-1763. [PMID: 15536068]

EC 5.1.3.23

Accepted name: UDP-2,3-diacetamido-2,3-dideoxyglucuronic acid 2-epimerase

Reaction: UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronate = UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronate

Glossary: UDP-α-D-GlcNAc3NAcA = UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid
UDP-α-D-ManNAc3NAcA = UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid

Other name(s): UDP-GlcNAc3NAcA 2-epimerase; UDP-α-D-GlcNAc3NAcA 2-epimerase; 2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid 2-epimerase; WbpI; WlbD

Systematic name: 2,3-diacetamido-2,3-dideoxy-α-D-glucuronate 2-epimerase

Comments: This enzyme participates in the biosynthetic pathway for UDP-α-D-ManNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid), an important precursor of the B-band lipopolysaccharide of Pseudomonas aeroginosa serotype O5 and of the band-A trisaccharide of Bordetella pertussis, both important respiratory pathogens [1]. The enzyme is highly specific as UDP-α-D-GlcNAc, UDP-α-D-GlcNAcA (UDP-2-acetamido-2-deoxy-α-D-glucuronic acid) and UDP-α-D-GlcNAc3NAc (UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucose) cannot act as substrates [1].

References:

1. Westman, E.L., McNally, D.J., Rejzek, M., Miller, W.L., Kannathasan, V.S., Preston, A., Maskell, D.J., Field, R.A., Brisson, J.R. and Lam, J.S. Identification and biochemical characterization of two novel UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid 2-epimerases from respiratory pathogens. Biochem. J. 405 (2007) 123-130. [PMID: 17346239]

2. Westman, E.L., McNally, D.J., Rejzek, M., Miller, W.L., Kannathasan, V.S., Preston, A., Maskell, D.J., Field, R.A., Brisson, J.R. and Lam, J.S. Erratum report: Identification and biochemical characterization of two novel UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid 2-epimerases from respiratory pathogens. Biochem. J. 405 (2007) 625 only.

3. Sri Kannathasan, V., Staines, A.G., Dong, C.J., Field, R.A., Preston, A.G., Maskell, D.J. and Naismith, J.H. Overexpression, purification, crystallization and data collection on the Bordetella pertussis wlbD gene product, a putative UDP-GlcNAc 2′-epimerase. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 1310-1312. [PMID: 11526328]

EC 6.1.1.26

Accepted name: pyrrolysine—tRNA^Pyl ligase

Reaction: ATP + L-pyrrolysine + tRNA^Pyl = AMP + diphosphate + L-pyrrolysyl-tRNA^Pyl

Glossary: pyrrolysine = N⁶-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine

Other name(s): PylS; pyrrolysyl-tRNA synthetase

Systematic name: L-pyrrolysine:tRNA^Pyl ligase (AMP-forming)

Comments: In organisms such as Methanosarcina barkeri that incorporate the modified amino acid pyrrolysine (Pyl) into certain methylamine methyltransferases, an unusual tRNA^Pyl, with a CUA anticodon, can be charged directly with pyrrolysine by this class II aminoacyl—tRNA ligase. The enzyme is specific for pyrrolysine as substrate as it cannot be replaced by lysine or any of the other natural amino acids [1].

References:

1. Blight, S.K., Larue, R.C., Mahapatra, A., Longstaff, D.G., Chang, E., Zhao, G., Kang, P.T., Green-Church, K.B., Chan, M.K. and Krzycki, J.A. Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431 (2004) 333-335. [PMID: 15329732]

2. Polycarpo, C., Ambrogelly, A., Bérubé, A., Winbush, S.M., McCloskey, J.A., Crain, P.F., Wood, J.L. and Söll, D. An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc. Natl. Acad. Sci. USA 101 (2004) 12450-12454. [PMID: 15314242]

3. Schimmel, P. and Beebe, K. Molecular biology: genetic code seizes pyrrolysine. Nature 431 (2004) 257-258. [PMID: 15372017]

EC 6.3.2.29

Accepted name: cyanophycin synthase (L-aspartate-adding)

Reaction: ATP + [L-Asp(4-L-Arg)]_n + L-Asp = ADP + phosphate + [L-Asp(4-L-Arg)]_n—L-Asp

For diagram click here.

Glossary: cyanophycin = [L-Asp(4-L-Arg)]_n = N-β-aspartylarginine = [L-4-(L-arginin-2-N-yl)aspartic acid]_n = poly{N⁴-[(1S)-1-carboxy-4-guanidinobutyl]-L-asparagine}

Other name(s): CphA (ambiguous); CphA1 (ambiguous); CphA2 (ambiguous); cyanophycin synthetase (ambiguous); multi-L-arginyl-poly-L-aspartate synthase (ambiguous)

Systematic name: cyanophycin:L-aspartate ligase (ADP-forming)

Comments: Requires Mg²⁺ for activity. Both this enzyme and EC 6.3.2.30, cyanophycin synthase (L-arginine-adding), are required for the elongation of cyanophycin, which is a protein-like cell inclusion that is unique to cyanobacteria and acts as a temporary nitrogen store [2]. Both enzymes are found in the same protein but have different active sites [2]. Both L-Asp and L-Arg must be present before either enzyme will display significant activity [2].

References:

1. Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308. Arch. Microbiol. 174 (2000) 297-306. [PMID: 11131019]

2. Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Purification of Synechocystis sp. strain PCC6308 cyanophycin synthetase and its characterization with respect to substrate and primer specificity. Appl. Environ. Microbiol. 67 (2001) 2176-2182. [PMID: 11319097]

3. Allen, M.M., Hutchison, F. and Weathers, P.J. Cyanophycin granule polypeptide formation and degradation in the cyanobacterium Aphanocapsa 6308. J. Bacteriol. 141 (1980) 687-693. [PMID: 6767688]

4. Berg, H., Ziegler, K., Piotukh, K., Baier, K., Lockau, W. and Volkmer-Engert, R. Biosynthesis of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin): mechanism of the cyanophycin synthetase reaction studied with synthetic primers. Eur. J. Biochem. 267 (2000) 5561-5570. [PMID: 10951215]

5. Ziegler, K., Deutzmann, R. and Lockau, W. Cyanophycin synthetase-like enzymes of non-cyanobacterial eubacteria: characterization of the polymer produced by a recombinant synthetase of Desulfitobacterium hafniense. Z. Naturforsch. [C] 57 (2002) 522-529. [PMID: 12132696]

6. Ziegler, K., Diener, A., Herpin, C., Richter, R., Deutzmann, R. and Lockau, W. Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Eur. J. Biochem. 254 (1998) 154-159. [PMID: 9652408]

EC 6.3.2.30

Accepted name: cyanophycin synthase (L-arginine-adding)

Reaction: ATP + [L-Asp(4-L-Arg)]_n—L-Asp + L-Arg = ADP + phosphate + [L-Asp(4-L-Arg)]_n+1

For diagram click here.

Glossary: cyanophycin = [L-Asp(4-L-Arg)]_n = N-β-aspartylarginine = [L-4-(L-arginin-2-N-yl)aspartic acid]_n = poly{N⁴-[(1S)-1-carboxy-4-guanidinobutyl]-L-asparagine}

Other name(s): CphA (ambiguous); CphA1 (ambiguous); CphA2 (ambiguous); cyanophycin synthetase (ambiguous); multi-L-arginyl-poly-L-aspartate synthase (ambiguous)

Systematic name: cyanophycin:L-arginine ligase (ADP-forming)

Comments: Requires Mg²⁺ for activity. Both this enzyme and EC 6.3.2.29, cyanophycin synthase (L-aspartate-adding), are required for the elongation of cyanophycin, which is a protein-like cell inclusion that is unique to cyanobacteria and acts as a temporary nitrogen store [2]. Both enzymes are found in the same protein but have different active sites [2]. Both L-Asp and L-Arg must be present before either enzyme will display significant activity [2]. Canavanine and lysine can be incoporated into the polymer instead of arginine [2].

References:

1. Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308. Arch. Microbiol. 174 (2000) 297-306. [PMID: 11131019]

2. Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Purification of Synechocystis sp. strain PCC6308 cyanophycin synthetase and its characterization with respect to substrate and primer specificity. Appl. Environ. Microbiol. 67 (2001) 2176-2182. [PMID: 11319097]

3. Allen, M.M., Hutchison, F. and Weathers, P.J. Cyanophycin granule polypeptide formation and degradation in the cyanobacterium Aphanocapsa 6308. J. Bacteriol. 141 (1980) 687-693. [PMID: 6767688]

4. Berg, H., Ziegler, K., Piotukh, K., Baier, K., Lockau, W. and Volkmer-Engert, R. Biosynthesis of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin): mechanism of the cyanophycin synthetase reaction studied with synthetic primers. Eur. J. Biochem. 267 (2000) 5561-5570. [PMID: 10951215]

5. Ziegler, K., Deutzmann, R. and Lockau, W. Cyanophycin synthetase-like enzymes of non-cyanobacterial eubacteria: characterization of the polymer produced by a recombinant synthetase of Desulfitobacterium hafniense. Z. Naturforsch. [C] 57 (2002) 522-529. [PMID: 12132696]

6. Ziegler, K., Diener, A., Herpin, C., Richter, R., Deutzmann, R. and Lockau, W. Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Eur. J. Biochem. 254 (1998) 154-159. [PMID: 9652408]

[EC 6.3.5.8 Transferred entry: Now EC 2.6.1.85, aminodeoxychorismate synthase. As ATP is not hydrolysed during the reaction, the classification of the enzyme as a ligase was incorrect. (EC 6.3.5.8 created 2003, deleted 2007)]