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

Proposed Changes to the Enzyme List

The entries below are additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Keith Tipton, Sinèad Boyce, Gerry Moss and Hal Dixon, with occasional help from other Committee members, and were put on the web by Gerry Moss. Comments and suggestions on these draft entries should be sent to Professor K.F. Tipton and Dr S. Boyce (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland) The entries were added on the date indicated and fully approved after a month.

Many thanks to those of you who have submitted details of new or missing enzymes, or updates to existing enzymes.

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


Contents

EC 1.1.1.295 momilactone-A synthase (22 April 2008)
EC 1.1.99.32 L-sorbose 1-dehydrogenase (8 February 2008)
EC 1.3.7.6 phycoerythrobilin synthase (22 April 2008)
EC 1.3.99.24 2-amino-4-deoxychorismate dehydrogenase (22 April 2008)
*EC 1.5.1.12 1-pyrroline-5-carboxylate dehydrogenase (8 February 2008)
*EC 2.1.1.70 8-hydroxyfuranocoumarin 8-O-methyltransferase (8 February 2008)
EC 2.1.1.93 deleted, identical to EC 2.1.1.70 (8 February 2008)
EC 2.3.1.185 tropine acyltransferase (22 April 2008)
EC 2.3.1.186 pseudotropine acyltransferase (22 April 2008)
EC 2.6.1.86 2-amino-4-deoxychorismate synthase (22 April 2008)
EC 2.7.1.161 CTP-dependent riboflavin kinase (22 April 2008)
EC 2.7.1.162 N-acetylhexosamine 1-kinase (22 April 2008)
EC 2.7.7.65 diguanylate cyclase (8 February 2008)
EC 3.1.4.52 cyclic-guanylate-specific phosphodiesterase (8 February 2008)
EC 3.2.1.165 exo-1,4-β-D-glucosaminidase (22 April 2008)
EC 3.4.22.68 Ulp1 peptidase (8 February 2008)
*EC 3.5.1.54 allophanate hydrolase (8 February 2008)
*EC 3.5.1.84 biuret amidohydrolase (8 February 2008)
EC 3.5.1.98 histone deacetylase (8 February 2008)
*EC 3.5.2.15 cyanuric acid amidohydrolase (8 February 2008)
EC 4.2.3.28 ent-cassa-12,15-diene synthase (22 April 2008)
EC 4.2.3.29 ent-sandaracopimaradiene synthase (22 April 2008)
EC 4.2.3.30 ent-pimara-8(14),15-diene synthase (22 April 2008)
EC 4.2.3.31 ent-pimara-9(11),15-diene synthase (22 April 2008)
EC 4.2.3.32 levopimaradiene synthase (22 April 2008)
EC 4.2.3.33 stemar-13-ene synthase (22 April 2008)
EC 4.2.3.34 stemod-13(17)-ene synthase (22 April 2008)
EC 4.2.3.35 syn-pimara-7,15-diene synthase (22 April 2008)
*EC 4.3.1.3 histidine ammonia-lyase (8 February 2008)
EC 4.3.1.5 transferred, now divided into EC 4.3.1.23, EC 4.3.1.24 and EC 4.3.1.25 (8 February 2008)
EC 4.3.1.23 tyrosine ammonia-lyase (8 February 2008)
EC 4.3.1.24 phenylalanine ammonia-lyase (8 February 2008)
EC 4.3.1.25 phenylalanine/tyrosine ammonia-lyase (8 February 2008)
EC 5.5.1.14 syn-copalyl diphosphate synthase (22 April 2008)

EC 1.1.1.295

Accepted name: momilactone-A synthase

Reaction: 3β-hydroxy-9β-pimara-7,15-diene-19,6β-olide + NAD(P)+ = momilactone A + NAD(P)H + H+

For diagram of reaction, click here

Other name(s): momilactone A synthase; OsMAS

Systematic name: 3β-hydroxy-9β-pimara-7,15-diene-19,6β-olide:NAD(P)+ oxidoreductase

Comments: The rice phytoalexin momilactone A is a diterpenoid secondary metabolite that is involved in the defense mechanism of the plant. Momilactone A is produced in response to attack by a pathogen through the perception of elicitor signal molecules such as chitin oligosaccharide, or after exposure to UV irradiation. The enzyme, which catalyzes the last step in the biosynthesis of momilactone A, can use both NAD+ and NADP+ but activity is higher with NAD+ [1].

References:

1. Atawong, A., Hasegawa, M. and Kodama, O. Biosynthesis of rice phytoalexin: enzymatic conversion of 3β-hydroxy-9β-pimara-7,15-dien-19,6β-olide to momilactone A. Biosci. Biotechnol. Biochem. 66 (2002) 566-570. [PMID: 12005050]

2. Shimura, K., Okada, A., Okada, K., Jikumaru, Y., Ko, K.W., Toyomasu, T., Sassa, T., Hasegawa, M., Kodama, O., Shibuya, N., Koga, J., Nojiri, H. and Yamane, H. Identification of a biosynthetic gene cluster in rice for momilactones. J. Biol. Chem. 282 (2007) 34013-34018. [PMID: 17872948]

[EC 1.1.1.295 created 2008]

EC 1.1.99.32

Accepted name: L-sorbose 1-dehydrogenase

Reaction: L-sorbose + acceptor = 1-dehydro-L-sorbose + reduced acceptor

Glossary: 1-dehydro-L-sorbose = L-sorbosone = 2-dehydro-L-gulose

Other name(s): SDH

Systematic name: L-sorbose:acceptor 1-oxidoreductase

Comments: The product, L-sorbosone, is an intermediate in bacterial 2-keto-L-gulonic-acid formation. The activity of this membrane-bound enzyme is stimulated by Fe(III) or Co2+ but is inhibited by Cu2+. The enzyme is highly specific for L-sorbose as other sugars, such as glucose, mannitol and sorbitol, are not substrates. Phenazine methosulfate and DCIP can act as artificial acceptors.

References:

1. Sugisawa, T., Hoshino, T., Nomura, S. and Fujiwara, A. Isolation and characterization of membrane-bound L-sorbose dehydrogenase from Gluconobacter melanogenus UV10. Agric. Biol. Chem. 55 (1991) 363-370.

[EC 1.1.99.32 created 2008]

EC 1.3.7.6

Accepted name: phycoerythrobilin synthase

Reaction: (3Z)-phycoerythrobilin + 2 oxidized ferredoxin = biliverdin IXα + 2 reduced ferredoxin

Other name(s): PebS

Systematic name: (3Z)-phycoerythrobilin:ferredoxin oxidoreductase (from biliverdin IXα)

Comments: This enzyme, from a cyanophage infecting oceanic cyanobacteria of the Prochlorococcus genus, uses a four-electron reduction to carry out the reactions catalysed by EC 1.3.7.2 (15,16-dihydrobiliverdin:ferredoxin oxidoreductase) and EC 1.3.7.3 (phycoerythrobilin:ferredoxin oxidoreductase). 15,16-Dihydrobiliverdin is formed as a bound intermediate. Free 15,16-dihydrobiliverdin can also act as a substrate to form phycoerythrobilin.

References:

1. Dammeyer, T., Bagby, S.C., Sullivan, M.B., Chisholm, S.W. and Frankenberg-Dinkel, N. Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria. Curr. Biol. 18 (2008) 442-448. [PMID: 18356052]

[EC 1.3.7.6 created 2008]

EC 1.3.99.24

Accepted name: 2-amino-4-deoxychorismate dehydrogenase

Reaction: (2S)-2-amino-4-deoxychorismate + FMN = 3-(1-carboxyvinyloxy)anthranilate + FMNH2

For diagram of reaction, click here

Glossary: (2S)-2-amino-4-deoxychorismate = (2S,3S)-3-(1-carboxyvinyloxy)-2,3-dihydroanthranilate
3-enolpyruvoylanthranilate = 3-(1-carboxyvinyloxy)anthranilate

Other name(s): ADIC dehydrogenase; 2-amino-2-deoxyisochorismate dehydrogenase; SgcG

Systematic name: (2S)-2-amino-4-deoxychorismate:FMN oxidoreductase

Comments: The sequential action of EC 2.6.1.86, 2-amino-4-deoxychorismate synthase and this enzyme leads to the formation of the benzoxazolinate moiety of the enediyne antitumour antibiotic C-1027 [1,2].

References:

1. Van Lanen, S.G., Lin, S. and Shen, B. Biosynthesis of the enediyne antitumor antibiotic C-1027 involves a new branching point in chorismate metabolism. Proc. Natl. Acad. Sci. USA 105 (2008) 494-499. [PMID: 18182490]

2. Yu, L., Mah, S., Otani, T. and Dedon, P. The benzoxazolinate of C-1027 confers intercalative DNA binding. J. Am. Chem. Soc. 117 (1995) 8877-8878.

[EC 1.3.99.24 created 2008]

*EC 1.5.1.12

Accepted name: 1-pyrroline-5-carboxylate dehydrogenase

Reaction: (S)-1-pyrroline-5-carboxylate + NAD(P)+ + 2 H2O = L-glutamate + NAD(P)H + H+

For diagram of reaction, click here

Other name(s): Δ1-pyrroline-5-carboxylate dehydrogenase; 1-pyrroline dehydrogenase; pyrroline-5-carboxylate dehydrogenase; pyrroline-5-carboxylic acid dehydrogenase; L-pyrroline-5-carboxylate-NAD+ oxidoreductase; 1-pyrroline-5-carboxylate:NAD+ oxidoreductase; Δ1-pyrroline-5-carboxylic acid dehydrogenase

Systematic name: (S)-1-pyrroline-5-carboxylate:NAD+ oxidoreductase

Comments: This enzyme can oxidize a number of 1-pyrrolines, e.g. 3-hydroxy-1-pyrroline-5-carboxylate is converted into 4-hydroxyglutamate and (R)-1-pyrroline-5-carboxylate is converted into D-glutamate. While NAD+ appears to be the better electron acceptor, NADP+ can also act, but more slowly [1,3]. In many organisms, ranging from bacteria to mammals, proline is oxidized to glutamate in a two-step process involving this enzyme and EC 1.5.99.8, proline dehydrogenase [3]. In many bacterial species, both activities are carried out by a single bifunctional enzyme [3,4].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, PDB, CAS registry number: 9054-82-4

References:

1. Adams, E. and Goldstone, A. Hydroxyproline metabolism. IV. Enzymatic synthesis of γ-hydroxyglutamate from Δ1-pyrroline-3-hydroxy-5-carboxylate. J. Biol. Chem. 235 (1960) 3504-3512. [PMID: 13681370]

2. Strecker, H.J. The interconversion of glutamic acid and proline. III. Δ1-Pyrroline-5-carboxylic acid dehydrogenase. J. Biol. Chem. 235 (1960) 3218-3223.

3. Forlani, G., Scainelli, D. and Nielsen, E. Δ1-Pyrroline-5-carboxylate dehydrogenase from cultured cells of potato (purification and properties). Plant Physiol. 113 (1997) 1413-1418. [PMID: 12223682]

4. Brown, E.D. and Wood, J.M. Redesigned purification yields a fully functional PutA protein dimer from Escherichia coli. J. Biol. Chem. 267 (1992) 13086-13092. [PMID: 1618807]

5. Inagaki, E., Ohshima, N., Sakamoto, K., Babayeva, N.D., Kato, H., Yokoyama, S. and Tahirov, T.H. New insights into the binding mode of coenzymes: structure of Thermus thermophilus Δ1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63:462 (2007). [PMID: 17554163]

[EC 1.5.1.12 created 1972, modified 2008]

*EC 2.1.1.70

Accepted name: 8-hydroxyfuranocoumarin 8-O-methyltransferase

Reaction: (1) S-adenosyl-L-methionine + an 8-hydroxyfurocoumarin = S-adenosyl-L-homocysteine + an 8-methoxyfurocoumarin (general reaction)
(2) S-adenosyl-L-methionine + xanthotoxol = S-adenosyl-L-homocysteine + xanthotoxin

For diagram of reaction, click here

Glossary: xanthotoxin = O-methylxanthotoxol = 8-methoxypsoralen
xanthotoxol = 8-hydroxypsoralen

Other name(s): furanocoumarin 8-methyltransferase; furanocoumarin 8-O-methyl-transferase; xanthotoxol 8-O-methyltransferase; XMT; 8-hydroxyfuranocoumarin 8-O-methyltransferase; SAM:xanthotoxol O-methyltransferase; S-adenosyl-L-methionine:8-hydroxyfuranocoumarin 8-O-methyltransferase; xanthotoxol methyltransferase; xanthotoxol O-methyltransferase; S-adenosyl-L-methionine:xanthotoxol O-methyltransferase; S-adenosyl-L-methionine-xanthotoxol O-methyltransferase

Systematic name: S-adenosyl-L-methionine:8-hydroxyfurocoumarin 8-O-methyltransferase

Comments: Converts xanthotoxol into xanthotoxin, which has therapeutic potential in the treatment of psoriasis as it has photosensitizing and antiproliferative activities [4]. Methylates the 8-hydroxy group of some hydroxy- and methylcoumarins, but has little activity on non-coumarin phenols (see also EC 2.1.1.69, 5-hydroxyfuranocoumarin 5-O-methyltransferase).

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, CAS registry number: 67339-13-3

References:

1. Thompson, H.J., Sharma, S.K. and Brown, S.A. O-Methyltransferases of furanocoumarin biosynthesis. Arch. Biochem. Biophys. 188 (1978) 272-281. [PMID: 28084]

2. Hauffe, K.D., Hahlbrock, K. and Scheel, D. Elicitor-stimulated furanocoumarin biosynthesis in cultured parsley cells - S-adenosyl-L-methionine-bergaptol and S-adenosyl-L-methionine-xanthotoxol O-methyltransferases. Z. Naturforsch. C: Biosci. 41 (1986) 228-239.

3. Sharma, S.K., Garrett, J.M. and Brown, S.A. Separation of the S-adenosylmethionine: 5- and 8-hydroxyfuranocoumarin O-methyltransferases of Ruta graveolens L. by general ligand affinity chromatography. Z. Naturforsch. [C] 34C (1979) 387-391. [PMID: 156999]

4. Hehmann, M., Lukačin, R., Ekiert, H. and Matern, U. Furanocoumarin biosynthesis in Ammi majus L. Cloning of bergaptol O-methyltransferase. Eur. J. Biochem. 271 (2004) 932-940. [PMID: 15009205]

Note For reference 4 an accent may not be seen. č is c-hacek.

[EC 2.1.1.70 created 1984, modified 2006 (EC 2.1.1.93 created 2006, incorporated 2008)]

[EC 2.1.1.93 Deleted entry: xanthotoxol O-methyltransferase. Enzyme is identical to EC 2.1.1.70, 8-hydroxyfuranocoumarin 8-O-methyltransferase. (EC 2.1.1.93 created 1989, deleted 2008)]

EC 2.3.1.185

Accepted name: tropine acyltransferase

Reaction: an acyl-CoA + tropine = CoA + an O-acyltropine

For diagram of reaction, click here

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

Other name(s): tropine:acyl-CoA transferase; acetyl-CoA:tropan-3-ol acyltransferase; tropine acetyltransferase; tropine tigloyltransferase; TAT

Systematic name: acyl-CoA:tropine O-acyltransferase

Comments: This enzyme exhibits absolute specificity for the endo/3α configuration found in tropine as pseudotropine (tropan-3β-ol; see EC 2.3.1.186, pseudotropine acyltransferase) is not a substrate [3]. Acts on a wide range of aliphatic acyl-CoA derivatives, with tigloyl-CoA and acetyl-CoA being the best substrates. It is probably involved in the formation of the tropane alkaloid littorine, which is a precursor of hyoscyamine [4].

References:

1. Robins, R.J., Bachmann, P., Robinson, T., Rhodes, M.J. and Yamada, Y. The formation of 3α- and 3β-acetoxytropanes by Datura stramonium transformed root cultures involves two acetyl-CoA-dependent acyltransferases. FEBS Lett. 292 (1991) 293-297. [PMID: 1959620]

2. Robins, R.J., Bachmann,P., Peerless, A.C.J. and Rabot, S. Esterification reactions in the biosynthesis of tropane alkaloids in transformed root cultures. Plant Cell, Tissue Organ Cult. 38 (1994) 241-247.

3. Boswell, H.D., Dräger, B., McLauchlan, W.R., Portsteffen, A., Robins, D.J., Robins, R.J. and Walton, N.J. Specificities of the enzymes of N-alkyltropane biosynthesis in Brugmansia and Datura. Phytochemistry 52 (1999) 871-878. [PMID: 10626376]

4. Li, R., Reed, D.W., Liu, E., Nowak, J., Pelcher, L.E., Page, J.E. and Covello, P.S. Functional genomic analysis of alkaloid biosynthesis in Hyoscyamus niger reveals a cytochrome P450 involved in littorine rearrangement. Chem. Biol. 13 (2006) 513-520. [PMID: 16720272]

[EC 2.3.1.185 created 2008]

EC 2.3.1.186

Accepted name: pseudotropine acyltransferase

Reaction: an acyl-CoA + pseudotropine = CoA + an O-acylpseudotropine

For diagram of reaction, click here

Glossary: tropine = tropan-3β-ol = 3β-hydroxytropane

Other name(s): pseudotropine:acyl-CoA transferase; tigloyl-CoA:pseudotropine acyltransferase; acetyl-CoA:pseudotropine acyltransferase; pseudotropine acetyltransferase; pseudotropine tigloyltransferase; PAT

Systematic name: acyl-CoA:pseudotropine O-acyltransferase

Comments: This enzyme exhibits absolute specificity for the exo/3β configuration found in pseudotropine as tropine (tropan-3α-ol; see EC 2.3.1.185, tropine acyltransferase) and nortropine are not substrates [1]. Acts on a wide range of aliphatic acyl-CoA derivatives, including acetyl-CoA, β-methylcrotonyl-CoA and tigloyl-CoA [1].

References:

1. Rabot, S., Peerless, A.C.J. and Robins, R.J. Tigloyl-CoA:pseudotropine acyltransferase — an enzyme of tropane alkaloid biosynthesis. Phytochemistry 39 (1995) 315-322.

2. Robins, R.J., Bachmann, P., Robinson, T., Rhodes, M.J. and Yamada, Y. The formation of 3α- and 3β-acetoxytropanes by Datura stramonium transformed root cultures involves two acetyl-CoA-dependent acyltransferases. FEBS Lett. 292 (1991) 293-297. [PMID: 1959620]

3. Robins, R.J., Bachmann,P., Peerless, A.C.J. and Rabot, S. Esterification reactions in the biosynthesis of tropane alkaloids in transformed root cultures. Plant Cell, Tissue Organ Cult. 38 (1994) 241-247.

4. Boswell, H.D., Dräger, B., McLauchlan, W.R., Portsteffen, A., Robins, D.J., Robins, R.J. and Walton, N.J. Specificities of the enzymes of N-alkyltropane biosynthesis in Brugmansia and Datura. Phytochemistry 52 (1999) 871-878. [PMID: 10626376]

[EC 2.3.1.186 created 2008]

EC 2.6.1.86

Accepted name: 2-amino-4-deoxychorismate synthase

Reaction: (2S)-2-amino-4-deoxychorismate + L-glutamate = chorismate + L-glutamine

For diagram of reaction, click here

Glossary: (2S)-2-amino-4-deoxychorismate = (2S,3S)-3-(1-carboxyvinyloxy)-2,3-dihydroanthranilate

Other name(s): ADIC synthase; 2-amino-2-deoxyisochorismate synthase; SgcD

Systematic name: (2S)-2-amino-4-deoxychorismate:2-oxoglutarate aminotransferase

Comments: Requires Mg2+. The reaction occurs in the reverse direction to that shown above. In contrast to most anthranilate-synthase I (ASI) homologues, this enzyme is not inhibited by tryptophan. In Streptomyces globisporus, the sequential action of this enzyme and EC 1.3.99.24, 2-amino-4-deoxychorismate dehydrogenase, leads to the formation of the benzoxazolinate moiety of the enediyne antitumour antibiotic C-1027 [1,2]. In certain Pseudomonads the enzyme participates in the biosynthesis of phenazine, a precursor for several compounds with antibiotic activity [3,4].

References:

1. Van Lanen, S.G., Lin, S. and Shen, B. Biosynthesis of the enediyne antitumor antibiotic C-1027 involves a new branching point in chorismate metabolism. Proc. Natl. Acad. Sci. USA 105 (2008) 494-499. [PMID: 18182490]

2. Yu, L., Mah, S., Otani, T. and Dedon, P. The benzoxazolinate of C-1027 confers intercalative DNA binding. J. Am. Chem. Soc. 117 (1995) 8877-8878.

3. McDonald, M., Mavrodi, D.V., Thomashow, L.S. and Floss, H.G. Phenazine biosynthesis in Pseudomonas fluorescens: branchpoint from the primary shikimate biosynthetic pathway and role of phenazine-1,6-dicarboxylic acid. J. Am. Chem. Soc. 123 (2001) 9459-9460. [PMID: 11562236]

4. Laursen, J.B. and Nielsen, J. Phenazine natural products: biosynthesis, synthetic analogues, and biological activity. Chem. Rev. 104 (2004) 1663-1686. [PMID: 15008629]

[EC 2.6.1.86 created 2008]

EC 2.7.1.161

Accepted name: CTP-dependent riboflavin kinase

Reaction: CTP + riboflavin = CDP + FMN

Other name(s): Methanocaldococcus jannaschii Mj0056; Mj0056

Systematic name: CTP:riboflavin 5'-phosphotransferase

Comments: This archaeal enzyme differs from EC 2.7.1.26, riboflavin kinase, in using CTP as the donor nucleotide. UTP, but not ATP or GTP, can also act as a phosphate donor but it is at least an order of magnitude less efficient than CTP.

References:

1. Ammelburg, M., Hartmann, M.D., Djuranovic, S., Alva, V., Koretke, K.K., Martin, J., Sauer, G., Truffault, V., Zeth, K., Lupas, A.N. and Coles, M. A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Structure 15 (2007) 1577-1590. [PMID: 18073108]

[EC 2.7.1.161 created 2008]

EC 2.7.1.162

Accepted name: N-acetylhexosamine 1-kinase

Reaction: ATP + N-acetyl-D-hexosamine = ADP + N-acetyl-α-D-hexosamine 1-phosphate

Other name(s): NahK; LnpB; N-acetylgalactosamine/N-acetylglucosamine 1-kinase

Systematic name: ATP:N-acetyl-D-hexosamine 1-phosphotransferase

Comments: This enzyme is involved in the lacto-N-biose I/galacto-N-biose degradation pathway in the probiotic bacterium Bifidobacterium longum. Differs from EC 2.7.1.157, N-acetylgalactosamine kinase, as it can phosphorylate both N-acetylgalactosamine and N-acetylglucosamine at similar rates. Also has some activity with N-acetyl-D-mannosamine, D-talose and D-mannose as substrate. ATP can be replaced by GTP or ITP but with decreased enzyme activity. Requires a divalent cation, with Mg2+ resulting in by far the greatest stimulation of enzyme activity.

References:

1. Nishimoto, M. and Kitaoka, M. Identification of N-acetylhexosamine 1-kinase in the complete lacto-N-biose I/galacto-N-biose metabolic pathway in Bifidobacterium longum. Appl. Environ. Microbiol. 73 (2007) 6444-6449. [PMID: 17720833]

[EC 2.7.1.162 created 2008]

EC 2.7.7.65

Accepted name: diguanylate cyclase

Reaction: 2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate

For diagram of reaction click here

Glossary: c-di-GMP = c-di-guanylate = cyclic di-3',5'-guanylate = cyclic-bis(3'→5') dimeric GMP

Other name(s): DGC; PleD

Systematic name: GTP:GTP guanylyltransferase

Comments: A GGDEF-domain-containing protein that requires Mg2+ or Mn2+ for activity. The enzyme can be activated by BeF3, a phosphoryl mimic, which results in dimerization [3]. Dimerization is required but is not sufficient for diguanylate-cyclase activity [3]. Cyclic di-3',5'-guanylate is an intracellular signalling molecule that controls motility and adhesion in bacterial cells. It was first identified as having a positive allosteric effect on EC 2.4.1.12, cellulose synthase (UDP-forming) [1].

References:

1. Ryjenkov, D.A., Tarutina, M., Moskvin, O.V. and Gomelsky, M. Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain. J. Bacteriol. 187 (2005) 1792-1798. [PMID: 15716451]

2. Méndez-Ortiz, M.M., Hyodo, M., Hayakawa, Y. and Membrillo-Hernández, J. Genome-wide transcriptional profile of Escherichia coli in response to high levels of the second messenger 3',5'-cyclic diguanylic acid. J. Biol. Chem. 281 (2006) 8090-8099. [PMID: 16418169]

3. Paul, R., Abel, S., Wassmann, P., Beck, A., Heerklotz, H. and Jenal, U. Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization. J. Biol. Chem. 282 (2007) 29170-29177. [PMID: 17640875]

[EC 2.7.7.65 created 2008]

EC 3.1.4.52

Accepted name: cyclic-guanylate-specific phosphodiesterase

Reaction: cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'→5')guanosine

For diagram of reaction click here

Glossary: c-di-GMP = c-di-guanylate = cyclic di-3',5'-guanylate = cyclic-bis(3'→5') dimeric GMP

Other name(s): cyclic bis(3→5')diguanylate phosphodiesterase; c-di-GMP-specific phosphodiesterase; c-di-GMP phosphodiesterase; phosphodiesterase; phosphodiesterase A1; PDEA1; VieA

Systematic name: cyclic bis(3→5')diguanylate 3-guanylylhydrolase

Comments: Requires Mg2+ or Mn2+ for activity and is inhibited by Ca2+ and Zn2+. Contains a heme unit. This enzyme linearizes cyclic di-3',5'-guanylate, the product of EC 2.7.7.65, diguanylate cyclase and an allosteric activator of EC 2.4.1.12, cellulose synthase (UDP-forming), rendering it inactive [1]. It is the balance between these two enzymes that determines the cellular level of c-di-GMP [1].

References:

1. Chang, A.L., Tuckerman, J.R., Gonzalez, G., Mayer, R., Weinhouse, H., Volman, G., Amikam, D., Benziman, M. and Gilles-Gonzalez, M.A. Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. Biochemistry 40 (2001) 3420-3426. [PMID: 11297407]

2. Christen, M., Christen, B., Folcher, M., Schauerte, A. and Jenal, U. Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP. J. Biol. Chem. 280 (2005) 30829-30837. [PMID: 15994307]

3. Schmidt, A.J., Ryjenkov, D.A. and Gomelsky, M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J. Bacteriol. 187 (2005) 4774-4781. [PMID: 15995192]

4. Tamayo, R., Tischler, A.D. and Camilli, A. The EAL domain protein VieA is a cyclic diguanylate phosphodiesterase. J. Biol. Chem. 280 (2005) 33324-33330. [PMID: 16081414]

[EC 3.1.4.52 created 2008]

EC 3.2.1.165

Accepted name: exo-1,4-β-D-glucosaminidase

Reaction: Hydrolysis of chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from the non-reducing termini

Glossary: GlcN = D-glucosamine = 2-amino-2-deoxy-D-glucopyranose
GlcNAc = N-acetyl-D-glucosamine

Other name(s): CsxA; GlcNase; exochitosanase; GlmA; exo-β-D-glucosaminidase

Systematic name: chitosan exo-1,4-β-D-glucosaminidase

Comments: Chitosan is a partially or totally N-deacetylated chitin derivative that is found in the cell walls of some phytopathogenic fungi and comprises D-glucosamine residues with a variable content of GlcNAc residues [4]. Acts specifically on chitooligosaccharides and chitosan, having maximal activity on chitotetraose, chitopentaose and their corresponding alcohols [1]. The enzyme can degrade GlcN-GlcNAc but not GlcNAc-GlcNAc [3]. A member of the glycoside hydrolase family 2 (GH-2) [4].

References:

1. Nanjo, F., Katsumi, R. and Sakai, K. Purification and characterization of an exo-β-D-glucosaminidase, a novel type of enzyme, from Nocardia orientalis. J. Biol. Chem. 265 (1990) 10088-10094. [PMID: 2351651]

2. Nogawa, M., Takahashi, H., Kashiwagi, A., Ohshima, K., Okada, H. and Morikawa, Y. Purification and characterization of exo-β-D-glucosaminidase from a cellulolytic fungus, Trichoderma reesei PC-3-7. Appl. Environ. Microbiol. 64 (1998) 890-895. [PMID: 16349528]

3. Fukamizo, T., Fleury, A., Côté, N., Mitsutomi, M. and Brzezinski, R. Exo-β-D-glucosaminidase from Amycolatopsis orientalis: catalytic residues, sugar recognition specificity, kinetics, and synergism. Glycobiology 16 (2006) 1064-1072. [PMID: 16877749]

4. Côté, N., Fleury, A., Dumont-Blanchette, E., Fukamizo, T., Mitsutomi, M. and Brzezinski, R. Two exo-β-D-glucosaminidases/exochitosanases from actinomycetes define a new subfamily within family 2 of glycoside hydrolases. Biochem. J. 394:675 (2006). [PMID: 16316314]

5. Ike, M., Isami, K., Tanabe, Y., Nogawa, M., Ogasawara, W., Okada, H. and Morikawa, Y. Cloning and heterologous expression of the exo-β-D-glucosaminidase-encoding gene (gls93) from a filamentous fungus, Trichoderma reesei PC-3-7. Appl. Microbiol. Biotechnol. 72 (2006) 687-695. [PMID: 16636831]

[EC 3.2.1.165 created 2008]

EC 3.4.22.68

Accepted name: Ulp1 peptidase

Reaction: Hydrolysis of the α-linked peptide bond in the sequence Gly-Gly┼Ala-Thr-Tyr at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptide, Smt3, leading to the mature form of the protein. A second reaction involves the formation of an ε-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine ε-amino group of the target protein

Other name(s): small ubiquitin-related modifier protein 1 conjugate proteinase; Smt3-protein conjugate proteinase; SUMO isopeptidase; SUMO protease; SUMO-1 conjugate proteinase; Sumo-1 hydrolase; SUMO-1-conjugate protease; SUMO-1-deconjugating enzyme; SUMO-specific protease; SUMO-specific proteinase; Ubl-specific protease 1; Ulp1; Ulp1 endopeptidase; Ulp1 protease

Comments: The enzyme from Saccharomyces cerevisiae can also recognize small ubiquitin-like modifier 1 (SUMO-1) from human as a substrate in both SUMO-processing (α-linked peptide bonds) and SUMO-deconjugation (ε-linked peptide bonds) reactions [1,2,3]. Ulp1 has several functions, including an essential role in chromosomal segregation and progression of the cell cycle through the G2/M phase of the cell cycle. Belongs in peptidase family C48.

References:

1. Lima, C.D. Ulp1 endopeptidase. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Eds), Handbook of Proteolytic Enzymes, 2nd edn, Elsevier, London, 2004, pp. 1340-1344.

2. Li, S.-J. and Hochstrasser, M. A new protease required for cell-cycle progression in yeast. Nature 398 (1999) 246-251. [PMID: 10094048]

3. Taylor, D.L., Ho, J.C., Oliver, A. and Watts, F.Z. Cell-cycle-dependent localisation of Ulp1, a Schizosaccharomyces pombe Pmt3 (SUMO)-specific protease. J. Cell Sci. 115 (2002) 1113-1122. [PMID: 11884512]

4. Li, S.-J. and Hochstrasser, M. The Ulp1 SUMO isopeptidase: distinct domains required for viability, nuclear envelope localization, and substrate specificity. J. Cell Biol. 160 (2003) 1069-1081. [PMID: 12654900]

5. Ihara, M., Koyama, H., Uchimura, Y., Saitoh, H. and Kikuchi, A. Noncovalent binding of small ubiquitin-related modifier (SUMO) protease to SUMO is necessary for enzymatic activities and cell growth. J. Biol. Chem. 282 (2007) 16465-16475. [PMID: 17428805]

6. Mukhopadhyay, D. and Dasso, M. Modification in reverse: the SUMO proteases. Trends Biochem. Sci. 32 (2007) 286-295. [PMID: 17499995]

[EC 3.4.22.68 created 2008]

*EC 3.5.1.54

Accepted name: allophanate hydrolase

Reaction: urea-1-carboxylate + H2O = 2 CO2 + 2 NH3

Glossary: allophanate = urea-1-carboxylate

Other name(s): allophanate lyase; AtzF; TrzF

Systematic name: urea-1-carboxylate amidohydrolase

Comments: Along with EC 3.5.2.15 (cyanuric acid amidohydrolase) and EC 3.5.1.84 (biuret amidohydrolase), this enzyme forms part of the cyanuric-acid metabolism pathway, which degrades s-triazide herbicides, such as atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-1,3,5-triazine], in bacteria. The yeast enzyme (but not that from green algae) also catalyses the reaction of EC 6.3.4.6, urea carboxylase, thus bringing about the hydrolysis of urea to CO2 and NH3 in the presence of ATP and bicarbonate. The enzyme from Pseudomonas sp. strain ADP has a narrow substrate specificity, being unable to use the structurally analogous compounds urea, hydroxyurea or methylcarbamate as substrate [6].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, UM-BBD, CAS registry number: 79121-96-3

References:

1. Maitz, G.S., Haas, E.M. and Castric, P.A. Purification and properties of the allophanate hydrolase from Chlamydomonas reinhardii. Biochim. Biophys. Acta 714 (1982) 486-491.

2. Roon, R.J. and Levenberg, B. Urea amidolyase. I. Properties of the enzyme from Candida utilis. J. Biol. Chem. 247 (1972) 4107-4113. [PMID: 4556303]

3. Sumrada, R.A. and Cooper, T.G. Urea carboxylase and allophanate hydrolase are components of a multifunctional protein in yeast. J. Biol. Chem. 257 (1982) 9119-9127. [PMID: 6124544]

4. Kanamori, T., Kanou, N., Kusakabe, S., Atomi, H. and Imanaka, T. Allophanate hydrolase of Oleomonas sagaranensis involved in an ATP-dependent degradation pathway specific to urea. FEMS Microbiol. Lett. 245 (2005) 61-65. [PMID: 15796980]

5. Cheng, G., Shapir, N., Sadowsky, M.J. and Wackett, L.P. Allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism. Appl. Environ. Microbiol. 71 (2005) 4437-4445. [PMID: 16085834]

6. Shapir, N., Sadowsky, M.J. and Wackett, L.P. Purification and characterization of allophanate hydrolase (AtzF) from Pseudomonas sp. strain ADP. J. Bacteriol. 187 (2005) 3731-3738. [PMID: 15901697]

7. Shapir, N., Cheng, G., Sadowsky, M.J. and Wackett, L.P. Purification and characterization of TrzF: biuret hydrolysis by allophanate hydrolase supports growth. Appl. Environ. Microbiol. 72 (2006) 2491-2495. [PMID: 16597948]

[EC 3.5.1.54 created 1986, modified 2008]

*EC 3.5.1.84

Accepted name: biuret amidohydrolase

Reaction: biuret + H2O = urea-1-carboxylate + NH3

Glossary: biuret = imidodicarbonic diamide
allophanate = urea-1-carboxylate

Systematic name: biuret amidohydrolase

Comments: Along with EC 3.5.2.15 (cyanuric acid amidohydrolase) and EC 3.5.1.54 (allophanate hydrolase), this enzyme forms part of the cyanuric-acid metabolism pathway, which degrades s-triazide herbicides, such as atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-1,3,5-triazine], in bacteria. Urea-1-carboxylate rather than urea (as was thought previously) is the 2-nitrogen intermediate in cyanuric-acid metabolism in bacteria [2]. The product, urea-1-carboxylate, can spontaneously decarboxylate under acidic conditions to form urea but, under physiological conditions, it can be converted into CO2 and ammonia by the action of EC 3.5.1.54 [2].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, UM-BBD CAS registry number:

References:

1. Cook, A.M., Beilstein, P., Grossenbacher, H. and Hutter, R. Ring cleavage and degradative pathway of cyanuric acid in bacteria. Biochem. J. 231 (1985) 25-30. [PMID: 3904735]

2. Cheng, G., Shapir, N., Sadowsky, M.J. and Wackett, L.P. Allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism. Appl. Environ. Microbiol. 71 (2005) 4437-4445. [PMID: 16085834]

3. Shapir, N., Sadowsky, M.J. and Wackett, L.P. Purification and characterization of allophanate hydrolase (AtzF) from Pseudomonas sp. strain ADP. J. Bacteriol. 187 (2005) 3731-3738. [PMID: 15901697]

[EC 3.5.1.84 created 2000, modified 2008]

EC 3.5.1.98

Accepted name: histone deacetylase

Reaction: Hydrolysis of an N6-acetyl-lysine residue of a histone to yield a deacetylated histone

Other name(s): HDAC

Systematic name: histone amidohydrolase

Comments: A class of enzymes that remove acetyl groups from N6-acetyl-lysine residues on a histone. The reaction of this enzyme is opposite to that of EC 2.3.1.48, histone acetyltransferase. Histone deacetylases (HDACs) can be organized into three classes, HDAC1, HDAC2 and HDAC3, depending on sequence similarity and domain organization. Histone acetylation plays an important role in regulation of gene expression. In eukaryotes, HDACs play a key role in the regulation of transcription and cell proliferation [4]. May be identical to EC 3.5.1.17, acyl-lysine deacylase.

References:

1. Krieger, D.E., Levine, R., Merrifield, R.B., Vidali, G. and Allfrey, V.G. Chemical studies of histone acetylation. Substrate specificity of a histone deacetylase from calf thymus nuclei. J. Biol. Chem. 249 (1974) 332-334. [PMID: 4855628]

2. Sanchez del Pino, M.M., Lopez-Rodas, G., Sendra, R. and Tordera, V. Properties of the yeast nuclear histone deacetylase. Biochem. J. 303 (1994) 723-729. [PMID: 7980438]

3. Ouaissi, M. and Ouaissi, A. Histone deacetylase enzymes as potential drug targets in cancer and parasitic diseases. J. Biomed. Biotechnol. 2006 (2006) 13474 only. [PMID: 16883049]

4. Song, Y.M., Kim, Y.S., Kim, D., Lee, D.S. and Kwon, H.J. Cloning, expression, and biochemical characterization of a new histone deacetylase-like protein from Thermus caldophilus GK24. Biochem. Biophys. Res. Commun. 361 (2007) 55-61. [PMID: 17632079]

5. Finnin, M.S., Donigian, J.R., Cohen, A., Richon, V.M., Rifkind, R.A., Marks, P.A., Breslow, R. and Pavletich, N.P. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 401 (1999) 188-193. [PMID: 10490031]

6. Phiel, C.J., Zhang, F., Huang, E.Y., Guenther, M.G., Lazar, M.A. and Klein, P.S. Histone deacetylase is a direct target of valproic acid, a potent anticonvulsant, mood stabilizer, and teratogen. J. Biol. Chem. 276 (2001) 36734-36741. [PMID: 11473107]

7. de Ruijter, A.J., van Gennip, A.H., Caron, H.N., Kemp, S. and van Kuilenburg, A.B. Histone deacetylases (HDACs): characterization of the classical HDAC family. Biochem. J. 370 (2003) 737-749. [PMID: 12429021]

[EC 3.5.1.98 created 2008]

*EC 3.5.2.15

Accepted name: cyanuric acid amidohydrolase

Reaction: cyanuric acid + H2O = biuret + CO2

Glossary: cyanuric acid = 1,3,5-triazine-2,4,6(1H,3H,5H)-trione = 2,4,6-trihydroxy-s-triazine
biuret = imidodicarbonic diamide

Other name(s): AtzD

Systematic name: cyanuric acid amidohydrolase

Comments: Along with EC 3.5.1.54 (allophanate hydrolase) and EC 3.5.1.84 (biuret amidohydrolase), this enzyme forms part of the cyanuric-acid metabolism pathway, which degrades s-triazide herbicides, such as atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-1,3,5-triazine], in bacteria. This is a key enzyme in the pathway, catalysing the ring cleavage of cyanuric acid. The enzyme is specific for cyanuric acid as substrate as neither the structurally related compounds ammeline (2,4-diamino-6-hydroxy-s-triazine) and ammelide (2-amino-4,6-dihydroxy-s-triazine) nor a number of pyrimidine compounds, such as uracil and cytosine, can act as substrates [3].

Links to other databases: BRENDA, ERGO, EXPASY, KEGG, UM-BBD, CAS registry number: 100785-00-0

References:

1. Eaton, R.W. and Karns, J.S. Cloning and comparison of the DNA encoding ammelide aminohydrolase and cyanuric acid amidohydrolase from three s-triazine-degrading bacterial strains. J. Bacteriol. 173 (1991) 1363-1366. [PMID: 1991731]

2. Eaton, R.W. and Karns, J.S. Cloning and analysis of s-triazine catabolic genes from Pseudomonas sp. strain NRRLB-12227. J. Bacteriol. 173 (1991) 1215-1222. [PMID: 1846859]

3. Karns, J.S. Gene sequence and properties of an s-triazine ring-cleavage enzyme from Pseudomonas sp. strain NRRLB-12227. Appl. Environ. Microbiol. 65 (1999) 3512-3517. [PMID: 10427042]

4. Fruchey, I., Shapir, N., Sadowsky, M.J. and Wackett, L.P. On the origins of cyanuric acid hydrolase: purification, substrates, and prevalence of AtzD from Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 69 (2003) 3653-3657. [PMID: 12788776]

[EC 3.5.2.15 created 2000, modified 2008]

EC 4.2.3.28

Accepted name: ent-cassa-12,15-diene synthase

Reaction: ent-copalyl diphosphate = ent-cassa-12,15-diene + diphosphate

For diagram of reaction, click here

Other name(s): OsDTC1; OsKS7

Systematic name: ent-copalyl-diphosphate diphosphate-lyase (ent-cassa-12,15-diene-forming)

Comments: This class I diterpene cyclase produces ent-cassa-12,15-diene, a precursor of the rice phytoalexins (#150;)-phytocassanes A-E. Phytoalexins are diterpenoid secondary metabolites that are involved in the defense mechanism of the plant, and are produced in response to pathogen attack through the perception of elicitor signal molecules such as chitin oligosaccharide, or after exposure to UV irradiation.

References:

1. Cho, E.M., Okada, A., Kenmoku, H., Otomo, K., Toyomasu, T., Mitsuhashi, W., Sassa, T., Yajima, A., Yabuta, G., Mori, K., Oikawa, H., Toshima, H., Shibuya, N., Nojiri, H., Omori, T., Nishiyama, M. and Yamane, H. Molecular cloning and characterization of a cDNA encoding ent-cassa-12,15-diene synthase, a putative diterpenoid phytoalexin biosynthetic enzyme, from suspension-cultured rice cells treated with a chitin elicitor. Plant J. 37 (2004) 1-8. [PMID: 14675427]

[EC 4.2.3.28 created 2008]

EC 4.2.3.29

Accepted name: ent-sandaracopimaradiene synthase

Reaction: ent-copalyl diphosphate = ent-sandaracopimara-8(14),15-diene + diphosphate

For diagram of reaction, click here

Other name(s): OsKS10; ent-sandaracopimara-8(14),15-diene synthase

Systematic name: ent-copalyl-diphosphate diphosphate-lyase [ent-sandaracopimara-8(14),15-diene-forming]

Comments: ent-Sandaracopimaradiene is a precursor of the rice oryzalexins A-F. Phytoalexins are diterpenoid secondary metabolites that are involved in the defense mechanism of the plant, and are produced in response to pathogen attack through the perception of elicitor signal molecules such as chitin oligosaccharide, or after exposure to UV irradiation. As a minor product, this enzyme also forms ent-pimara-8(14),15-diene, which is the sole product of EC 4.2.3.30, ent-pimara-8(14),15-diene synthase. ent-Pimara-8(14),15-diene is not a precursor in the biosynthesis of either gibberellins or phytoalexins [2].

References:

1. Otomo, K., Kanno, Y., Motegi, A., Kenmoku, H., Yamane, H., Mitsuhashi, W., Oikawa, H., Toshima, H., Itoh, H., Matsuoka, M., Sassa, T. and Toyomasu, T. Diterpene cyclases responsible for the biosynthesis of phytoalexins, momilactones A, B, and oryzalexins A-F in rice. Biosci. Biotechnol. Biochem. 68 (2004) 2001-2006. [PMID: 15388982]

2. Kanno, Y., Otomo, K., Kenmoku, H., Mitsuhashi, W., Yamane, H., Oikawa, H., Toshima, H., Matsuoka, M., Sassa, T. and Toyomasu, T. Characterization of a rice gene family encoding type-A diterpene cyclases. Biosci. Biotechnol. Biochem. 70 (2006) 1702-1710. [PMID: 16861806]

[EC 4.2.3.29 created 2008]

EC 4.2.3.30

Accepted name: ent-pimara-8(14),15-diene synthase

Reaction: ent-copalyl diphosphate = ent-pimara-8(14),15-diene + diphosphate

For diagram of reaction, click here

Other name(s): OsKS5

Systematic name: ent-copalyl-diphosphate diphosphate-lyase [ent-pimara-8(14),15-diene-forming]

Comments: Unlike EC 4.2.3.29, ent-sandaracopimaradiene synthase, which can produce both ent-sandaracopimaradiene and ent-pimara-8(14),15-diene, this diterpene cyclase produces only ent-pimara-8(14),15-diene. ent-Pimara-8(14),15-diene is not a precursor in the biosynthesis of either gibberellins or phytoalexins.

References:

1. Kanno, Y., Otomo, K., Kenmoku, H., Mitsuhashi, W., Yamane, H., Oikawa, H., Toshima, H., Matsuoka, M., Sassa, T. and Toyomasu, T. Characterization of a rice gene family encoding type-A diterpene cyclases. Biosci. Biotechnol. Biochem. 70 (2006) 1702-1710. [PMID: 16861806]

[EC 4.2.3.30 created 2008]

EC 4.2.3.31

Accepted name: ent-pimara-9(11),15-diene synthase

Reaction: ent-copalyl diphosphate = ent-pimara-9(11),15-diene + diphosphate

For diagram of reaction, click here

Other name(s): PMD synthase

Systematic name: ent-copalyl-diphosphate diphosphate-lyase [ent-pimara-9(11),15-diene-forming]

Comments: This enzyme is involved in the biosynthesis of the diterpenoid viguiepinol and requires Mg2+, Co2+, Zn2+ or Ni2+ for activity.

References:

1. Ikeda, C., Hayashi, Y., Itoh, N., Seto, H. and Dairi, T. Functional analysis of eubacterial ent-copalyl diphosphate synthase and pimara-9(11),15-diene synthase with unique primary sequences. J. Biochem. 141 (2007) 37-45. [PMID: 17148547]

[EC 4.2.3.31 created 2008]

EC 4.2.3.32

Accepted name: levopimaradiene synthase

Reaction: copalyl diphosphate = abieta-8(14),12-diene + diphosphate

Glossary: levopimaradiene = ent-abieta-8(14),12-diene

Other name(s): PtTPS-LAS; LPS

Systematic name: ent-copalyl-diphosphate diphosphate-lyase [ent-abieta-8(14),12-diene-forming]

Comments: Levopimaradiene is widely distributed in higher plants. In Ginkgo, it catalyses the initial cyclization step in the biosynthesis of ginkolides, a structurally unique family of diterpenoids that are highly specific platelet-activating-factor receptor antagonists [1]. In some species the enzyme also forms abietadiene, palustradiene, and neoabietadiene [2].

References:

1. Schepmann, H.G., Pang, J. and Matsuda, S.P. Cloning and characterization of Ginkgo biloba levopimaradiene synthase which catalyzes the first committed step in ginkgolide biosynthesis. Arch. Biochem. Biophys. 392 (2001) 263-269. [PMID: 11488601]

2. Ro, D.K. and Bohlmann, J. Diterpene resin acid biosynthesis in loblolly pine (Pinus taeda): functional characterization of abietadiene/levopimaradiene synthase (PtTPS-LAS) cDNA and subcellular targeting of PtTPS-LAS and abietadienol/abietadienal oxidase (PtAO, CYP720B1). Phytochemistry 67 (2006) 1572-1578. [PMID: 16497345]

[EC 4.2.3.32 created 2008]

EC 4.2.3.33

Accepted name: stemar-13-ene synthase

Reaction: 9α-copalyl diphosphate = stemar-13-ene + diphosphate

For diagram of reaction, click here

Glossary: syn-copalyl diphosphate = 9α-copalyl diphosphate

Other name(s): OsDTC2; OsK8; OsKL8; OsKS8; stemarene synthase; syn-stemar-13-ene synthase

Systematic name: 9α-copalyl-diphosphate diphosphate-lyase (stemar-13-ene-forming)

Comments: This diterpene cyclase produces stemar-13-ene, a putative precursor of the rice phytoalexin oryzalexin S. Phytoalexins are diterpenoid secondary metabolites that are involved in the defense mechanism of the plant, and are produced in response to pathogen attack through the perception of elicitor signal molecules such as chitin oligosaccharide, or after exposure to UV irradiation.

References:

1. Mohan, R.S., Yee, N.K., Coates, R.M., Ren, Y.Y., Stamenkovic, P., Mendez, I. and West, C.A. Biosynthesis of cyclic diterpene hydrocarbons in rice cell suspensions: conversion of 9,10-syn-labda-8(17),13-dienyl diphosphate to 9β-pimara-7,15-diene and stemar-13-ene. Arch. Biochem. Biophys. 330 (1996) 33-47. [PMID: 8651702]

2. Nemoto, T., Cho, E.M., Okada, A., Okada, K., Otomo, K., Kanno, Y., Toyomasu, T., Mitsuhashi, W., Sassa, T., Minami, E., Shibuya, N., Nishiyama, M., Nojiri, H. and Yamane, H. Stemar-13-ene synthase, a diterpene cyclase involved in the biosynthesis of the phytoalexin oryzalexin S in rice. FEBS Lett. 571 (2004) 182-186. [PMID: 15280039]

[EC 4.2.3.33 created 2008]

EC 4.2.3.34

Accepted name: stemod-13(17)-ene synthase

Reaction: 9α-copalyl diphosphate = stemod-13(17)-ene + diphosphate

For diagram of reaction, click here

Glossary: syn-copalyl diphosphate = 9α-copalyl diphosphate
exo-stemodene = stemod-13(17)-ene

Other name(s): OsKSL11; stemodene synthase

Systematic name: 9α-copalyl-diphosphate diphosphate-lyase [stemod-13(17)-ene-forming]

Comments: This enzyme catalyses the committed step in the biosynthesis of the stemodane family of diterpenoid secondary metabolites, some of which possess mild antiviral activity. The enzyme also produces stemod-12-ene and stemar-13-ene as minor products.

References:

1. Morrone, D., Jin, Y., Xu, M., Choi, S.Y., Coates, R.M. and Peters, R.J. An unexpected diterpene cyclase from rice: functional identification of a stemodene synthase. Arch. Biochem. Biophys. 448 (2006) 133-140. [PMID: 16256063]

[EC 4.2.3.34 created 2008]

EC 4.2.3.35

Accepted name: syn-pimara-7,15-diene synthase

Reaction: 9α-copalyl diphosphate = 9β-pimara-7,15-diene + diphosphate

For diagram of reaction, click here

Glossary: syn-copalyl diphosphate = 9α-copalyl diphosphate
syn-pimara-7,15-diene = 9β-pimara-7,15-diene

Other name(s): 9β-pimara-7,15-diene synthase; OsDTS2; OsKS4

Systematic name: 9α-copalyl-diphosphate diphosphate-lyase (9β-pimara-7,15-diene-forming)

Comments: This enzyme is a class I terpene synthase [1]. 9β-Pimara-7,15-diene is a precursor of momilactones A and B, rice diterpenoid phytoalexins that are produced in response to attack (by a pathogen, elicitor or UV irradiation) and are involved in the defense mechanism of the plant. Momilactone B can also act as an allochemical, being constitutively produced in the root of the plant and secreted to the rhizosphere where it suppresses the growth of neighbouring plants and soil microorganisms [1].

References:

1. Wilderman, P.R., Xu, M., Jin, Y., Coates, R.M. and Peters, R.J. Identification of syn-pimara-7,15-diene synthase reveals functional clustering of terpene synthases involved in rice phytoalexin/allelochemical biosynthesis. Plant Physiol. 135 (2004) 2098-2105. [PMID: 15299118]

2. Otomo, K., Kanno, Y., Motegi, A., Kenmoku, H., Yamane, H., Mitsuhashi, W., Oikawa, H., Toshima, H., Itoh, H., Matsuoka, M., Sassa, T. and Toyomasu, T. Diterpene cyclases responsible for the biosynthesis of phytoalexins, momilactones A, B, and oryzalexins A-F in rice. Biosci. Biotechnol. Biochem. 68 (2004) 2001-2006. [PMID: 15388982]

[EC 4.2.3.35 created 2008]

*EC 4.3.1.3

Accepted name: histidine ammonia-lyase

Reaction: L-histidine = urocanate + NH3

For diagram of reaction click here

Glossary: urocanate = (E)-3-(imidazol-4-yl)propenoate

Other name(s): histidase; histidinase; histidine α-deaminase; L-histidine ammonia-lyase

Systematic name: L-histidine ammonia-lyase (urocanate-forming)

Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.23 (tyrosine ammonia-lyase), EC 4.3.1.24 (phenylalanine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [4]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [5]. This enzyme catalyses the first step in the degradation of histidine and the product, urocanic acid, is further metabolized to glutamate [2,3].

Links to other databases: BRENDA, ERGO, EXPASY, GTD, KEGG, PDB, CAS registry number: 9013-75-6

References:

1. Mehler, A.H. and Tabor, H. Deamination of histidine to form urocanic acid in liver. J. Biol. Chem. 201 (1953) 775-784. [PMID: 13061415]

2. Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317-1326. [PMID: 17185227]

3. Poppe, L. and Rétey, J. Friedel-Crafts-type mechanism for the enzymatic elimination of ammonia from histidine and phenylalanine. Angew. Chem. Int. Ed. Engl. 44 (2005) 3668-3688. [PMID: 15906398]

4. Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327-1338. [PMID: 17185228]

5. Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355-5361. [PMID: 10220322]

[EC 4.3.1.3 created 1961, modified 2008]

[EC 4.3.1.5 Transferred entry: phenylalanine ammonia-lyase. Now divided into EC 4.3.1.23 (tyrosine ammonia-lyase), EC 4.3.1.24 (phenylalanine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). (EC 4.3.1.5 created 1965, deleted 2008)]

EC 4.3.1.23

Accepted name: tyrosine ammonia-lyase

Reaction: L-tyrosine = trans-p-hydroxycinnamate + NH3

Other name(s): TAL; tyrase; L-tyrosine ammonia-lyase

Systematic name: L-tyrosine ammonia-lyase (trans-p-hydroxycinnamate-forming)

Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase), EC 4.3.1.24 (phenylalanine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [1]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [3]. The enzyme is far more active with tyrosine than with phenylalanine as substrate, but the substrate specificity can be switched by mutation of a single amino acid (H89F) in the enzyme from the bacterium Rhodobacter sphaeroides [1,2].

References:

1. Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327-1338. [PMID: 17185228]

2. Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317-1326. [PMID: 17185227]

3. Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355-5361. [PMID: 10220322]

[EC 4.3.1.23 created 2008 (EC 4.3.1.5 created 1965, part-incorporated 2008)]

EC 4.3.1.24

Accepted name: phenylalanine ammonia-lyase

Reaction: L-phenylalanine = trans-cinnamate + NH3

For diagram of reaction click here

Other name(s): phenylalanine deaminase; phenylalanine ammonium-lyase; PAL; L-phenylalanine ammonia-lyase; Phe ammonia-lyase

Systematic name: L-phenylalanine ammonia-lyase (trans-cinnamate-forming)

Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase) and EC 4.3.1.23 (tyrosine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [3]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [9]. The enzyme from some species is highly specific for phenylalanine [7,8].

References:

1. Koukol, J. and Conn, E.E. The metabolism of aromatic compounds in higher plants. IV. Purification and properties of the phenylalanine deaminase of Hordeum vulgare. J. Biol. Chem. 236 (1961) 2692-2698. [PMID: 14458851]

2. Young, M.R. and Neish, A.C. Properties of the ammonia-lyases deaminating phenylalanine and related compounds in Triticum sestivum and Pteridium aquilinum. Phytochemistry 5 (1966) 1121-1132.

3. Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327-1338. [PMID: 17185228]

4. Calabrese, J.C., Jordan, D.B., Boodhoo, A., Sariaslani, S. and Vannelli, T. Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Biochemistry 43 (2004) 11403-11416. [PMID: 15350127]

5. Ritter, H. and Schulz, G.E. Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase. Plant Cell 16 (2004) 3426-3436. [PMID: 15548745]

6. Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317-1326. [PMID: 17185227]

7. Appert, C., Logemann, E., Hahlbrock, K., Schmid, J. and Amrhein, N. Structural and catalytic properties of the four phenylalanine ammonia-lyase isoenzymes from parsley (Petroselinum crispum Nym.). Eur. J. Biochem. 225 (1994) 491-499. [PMID: 7925471]

8. Cochrane, F.C., Davin, L.B. and Lewis, N.G. The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry 65 (2004) 1557-1564. [PMID: 15276452]

9. Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355-5361. [PMID: 10220322]

[EC 4.3.1.24 created 2008 (EC 4.3.1.5 created 1965, part-incorporated 2008)]

EC 4.3.1.25

Accepted name: phenylalanine/tyrosine ammonia-lyase

Reaction: (1) L-phenylalanine = trans-cinnamate + NH3
(2) L-tyrosine = trans-p-hydroxycinnamate + NH3

Other name(s): PTAL; bifunctional PAL

Systematic name: L-phenylalanine(or L-tyrosine):trans-cinnamate(or trans-p-hydroxycinnamate) ammonia-lyase

Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase), EC 4.3.1.23 (tyrosine ammonia-lyase) and EC 4.3.1.24 (phenylalanine ammonia-lyase). The enzyme from some monocots, including maize, and from the yeast Rhodosporidium toruloides, deaminate L-phenylalanine and L-tyrosine with similar catalytic efficiency [3]. The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [3]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [4].

References:

1. Rösler, J., Krekel, F., Amrhein, N. and Schmid, J. Maize phenylalanine ammonia-lyase has tyrosine ammonia-lyase activity. Plant Physiol. 113 (1997) 175-179. [PMID: 9008393]

2. Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317-1326. [PMID: 17185227]

3. Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327-1338. [PMID: 17185228]

4. Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355-5361. [PMID: 10220322]

[EC 4.3.1.25 created 2008 (EC 4.3.1.5 created 1965, part-incorporated 2008)]

EC 5.5.1.14

Accepted name: syn-copalyl diphosphate synthase

Reaction: geranylgeranyl diphosphate = 9α-copalyl diphosphate

For diagram of reaction, click here

Glossary: syn-copalyl diphosphate = 9α-copalyl diphosphate

Other name(s): OsCyc1; OsCPSsyn; syn-CPP synthase

Systematic name: 9α-copalyl-diphosphate lyase (decyclizing)

Comments: Requires a divalent metal ion, preferably Mg2+, for activity. This class II terpene synthase produces syn-copalyl diphosphate, a precursor of several rice phytoalexins, including oryzalexin S and momilactones A and B. Phytoalexins are diterpenoid secondary metabolites that are involved in the defense mechanism of the plant, and are produced in response to pathogen attack through the perception of elicitor signal molecules such as chitin oligosaccharide, or after exposure to UV irradiation. The enzyme is constitutively expressed in the roots of plants where one of its products, momilactone B, acts as an allelochemical (a molecule released into the environment to suppress the growth of neighbouring plants). In other tissues the enzyme is upregulated by conditions that stimulate the biosynthesis of phytoalexins.

References:

1. Otomo, K., Kenmoku, H., Oikawa, H., Konig, W.A., Toshima, H., Mitsuhashi, W., Yamane, H., Sassa, T. and Toyomasu, T. Biological functions of ent- and syn-copalyl diphosphate synthases in rice: key enzymes for the branch point of gibberellin and phytoalexin biosynthesis. Plant J. 39 (2004) 886-893. [PMID: 15341631]

2. Xu, M., Hillwig, M.L., Prisic, S., Coates, R.M. and Peters, R.J. Functional identification of rice syn-copalyl diphosphate synthase and its role in initiating biosynthesis of diterpenoid phytoalexin/allelopathic natural products. Plant J. 39 (2004) 309-318. [PMID: 15255861]

[EC 5.5.1.14 created 2008]


Return to Enzymes Home Page.