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.
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]
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.
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]
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.
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]
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 2.1.1.93 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)]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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 4.3.1.5 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)]
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]
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]
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]
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]