The Enzyme Database

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EC 1.1.1.398     
Accepted name: 2-glutathionyl-2-methylbut-3-en-1-ol dehydrogenase
Reaction: 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol + 2 NAD+ + H2O = 2-(glutathion-S-yl)-2-methylbut-3-enoate + 2 NADH + 2 H+ (overall reaction)
(1a) 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol + NAD+ = 2-(glutathion-S-yl)-2-methylbut-3-enal + NADH + H+
(1b) 2-(glutathion-S-yl)-2-methylbut-3-enal + NAD+ + H2O = 2-(glutathion-S-yl)-2-methylbut-3-enoate + NADH + H+
For diagram of isoprene biosynthesis and metabolism, click here
Other name(s): isoH (gene name); 4-hydroxy-3-glutathionyl-3-methylbut-1-ene dehydrogenase
Systematic name: 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol:NAD+ oxidoreductase
Comments: The enzyme, characterized from the bacterium Rhodococcus sp. AD45, is involved in isoprene degradation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  van Hylckama Vlieg, J.E., Kingma, J., Kruizinga, W. and Janssen, D.B. Purification of a glutathione S-transferase and a glutathione conjugate-specific dehydrogenase involved in isoprene metabolism in Rhodococcus sp. strain AD45. J. Bacteriol. 181 (1999) 2094–2101. [PMID: 10094686]
[EC 1.1.1.398 created 2016]
 
 
EC 1.3.1.94     
Accepted name: polyprenol reductase
Reaction: ditrans,polycis-dolichol + NADP+ = ditrans,polycis-polyprenol + NADPH + H+
Other name(s): SRD5A3 (gene name); DFG10 (gene name)
Systematic name: ditrans,polycis-dolichol:NADP+ 2,3-oxidoreductase
Comments: The reaction occurs in the reverse direction with reduction of the terminal double bond next to the alcohol group. Isolated from human fetal brain tissue but present in all eukaryotes. In mammalian cells dolichols are predominantly 18-21 isoprene units in length.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sagami, H., Kurisaki, A. and Ogura, K. Formation of dolichol from dehydrodolichol is catalyzed by NADPH-dependent reductase localized in microsomes of rat liver. J. Biol. Chem. 268 (1993) 10109–10113. [PMID: 8486680]
2.  Cantagrel, V., Lefeber, D.J., Ng, B.G., Guan, Z., Silhavy, J.L., Bielas, S.L., Lehle, L., Hombauer, H., Adamowicz, M., Swiezewska, E., De Brouwer, A.P., Blumel, P., Sykut-Cegielska, J., Houliston, S., Swistun, D., Ali, B.R., Dobyns, W.B., Babovic-Vuksanovic, D., van Bokhoven, H., Wevers, R.A., Raetz, C.R., Freeze, H.H., Morava, E., Al-Gazali, L. and Gleeson, J.G. SRD5A3 is required for converting polyprenol to dolichol and is mutated in a congenital glycosylation disorder. Cell 142 (2010) 203–217. [DOI] [PMID: 20637498]
[EC 1.3.1.94 created 2012]
 
 
EC 1.3.99.38     
Accepted name: menaquinone-9 β-reductase
Reaction: menaquinone-9 + reduced acceptor = β-dihydromenaquinone-9 + acceptor
For diagram of vitamin K biosynthesis, click here
Glossary: β-dihydromenaquinone-9 = MK-9(II-H2) = 2-methyl-3-[(2E,10E,14E,18E,22E,26E,30E,33E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,10,14,18,22,26,30,33-octaen-1-yl]naphthalene-1,4-dione
Other name(s): MenJ
Systematic name: menaquinone-9 oxidoreductase (β-dihydromenaquinone-9-forming)
Comments: The enzyme from the bacterium Mycobacterium tuberculosis reduces the β-isoprene unit of menaquinone-9, forming the predominant form of menaquinone found in mycobacteria. Contains FAD.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Upadhyay, A., Fontes, F.L., Gonzalez-Juarrero, M., McNeil, M.R., Crans, D.C., Jackson, M. and Crick, D.C. Partial saturation of menaquinone in Mycobacterium tuberculosis: function and essentiality of a novel reductase, MenJ. ACS Cent. Sci. 1 (2015) 292–302. [DOI] [PMID: 26436137]
[EC 1.3.99.38 created 2017]
 
 
EC 1.13.11.85     
Accepted name: exo-cleaving rubber dioxygenase
Reaction: cis-1,4-polyisoprene + n O2 = n (4Z,8Z)-4,8-dimethyl-12-oxotrideca-4,8-dienal
For diagram of all-cis-polyprenyl diphosphate, click here
Other name(s): roxA (gene name); heme-dependent rubber oxygenase (ambiguous)
Systematic name: cis-1,4-polyisoprene:oxygen dioxygenase [(4Z,8Z)-4,8-dimethyl-12-oxotrideca-4,8-dienal-forming]
Comments: The enzyme, studied mainly from the bacterium Xanthomonas sp. 35Y, catalyses the cleavage of the double bonds in natural and synthetic rubber (cis-1,4-polyisoprene polymers), generating ends that contain ketone and aldehyde groups. The enzyme from Xanthomonas sp. 35Y contains two c-type cytochromes. It attacks the substrate from its end, producing a single product of 15 carbons.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Tsuchii, A. and Takeda, K. Rubber-degrading enzyme from a bacterial culture. Appl. Environ. Microbiol. 56 (1990) 269–274. [PMID: 16348100]
2.  Jendrossek, D. and Reinhardt, S. Sequence analysis of a gene product synthesized by Xanthomonas sp. during growth on natural rubber latex. FEMS Microbiol. Lett. 224 (2003) 61–65. [DOI] [PMID: 12855168]
3.  Braaz, R., Fischer, P. and Jendrossek, D. Novel type of heme-dependent oxygenase catalyzes oxidative cleavage of rubber (poly-cis-1,4-isoprene). Appl. Environ. Microbiol. 70 (2004) 7388–7395. [DOI] [PMID: 15574940]
4.  Braaz, R., Armbruster, W. and Jendrossek, D. Heme-dependent rubber oxygenase RoxA of Xanthomonas sp. cleaves the carbon backbone of poly(cis-1,4-Isoprene) by a dioxygenase mechanism. Appl. Environ. Microbiol. 71 (2005) 2473–2478. [DOI] [PMID: 15870336]
5.  Seidel, J., Schmitt, G., Hoffmann, M., Jendrossek, D. and Einsle, O. Structure of the processive rubber oxygenase RoxA from Xanthomonas sp. Proc. Natl. Acad. Sci. USA 110 (2013) 13833–13838. [DOI] [PMID: 23922395]
6.  Birke, J. and Jendrossek, D. Rubber oxygenase and latex clearing protein cleave rubber to different products and use different cleavage mechanisms. Appl. Environ. Microbiol. 80 (2014) 5012–5020. [DOI] [PMID: 24907333]
[EC 1.13.11.85 created 2018]
 
 
EC 1.13.11.87     
Accepted name: endo-cleaving rubber dioxygenase
Reaction: Cleavage of cis-1,4-polyisoprene polymers into a mixture of compounds, including a C20 compound ((4Z,8Z,12Z,16Z,20Z,24Z)-4,8,12,16,20,24-hexamethyl-28-oxononacosa-4,8,12,16,20,24-hexaenal), a C25 compound ((4Z,8Z,12Z,16Z,20Z)-4,8,12,16,20-pentamethyl-24-oxopentacosa-4,8,12,16,20-pentaenal), a C30 compound ((4Z,8Z,12Z,16Z)-4,8,12,16-tetramethyl-20-oxohenicosa-4,8,12,16-tetraenal), and larger isoprenologes such as C35, C40, C45, and higher analogues.
For diagram of all-cis-polyprenyl diphosphate, click here
Other name(s): latex clearing protein; lcp (gene name); roxB (gene name)
Systematic name: cis-1,4-polyisoprene:oxygen dioxygenase (endo-cleaving)
Comments: The enzyme catalyses the cleavage of the double bonds in natural and synthetic rubber, producing a mixture of C20, C25, C30, and higher oligo-isoprenoids with ketone and aldehyde groups at their ends. Two unrelated bacterial enzymes are known to possess this activity - the enzyme from Streptomyces sp. K30 (Lcp) contains a b-type cytochrome, while the enzyme from Xanthomonas sp. 35Y, (RoxB) contains two c-type cytochromes. Both enzymes attack the substrate at random locations, and are not able to cleave the C35 or smaller products into shorter fragments.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Tsuchii, A. and Takeda, K. Rubber-degrading enzyme from a bacterial culture. Appl. Environ. Microbiol. 56 (1990) 269–274. [PMID: 16348100]
2.  Jendrossek, D. and Reinhardt, S. Sequence analysis of a gene product synthesized by Xanthomonas sp. during growth on natural rubber latex. FEMS Microbiol. Lett. 224 (2003) 61–65. [DOI] [PMID: 12855168]
3.  Braaz, R., Fischer, P. and Jendrossek, D. Novel type of heme-dependent oxygenase catalyzes oxidative cleavage of rubber (poly-cis-1,4-isoprene). Appl. Environ. Microbiol. 70 (2004) 7388–7395. [DOI] [PMID: 15574940]
4.  Braaz, R., Armbruster, W. and Jendrossek, D. Heme-dependent rubber oxygenase RoxA of Xanthomonas sp. cleaves the carbon backbone of poly(cis-1,4-Isoprene) by a dioxygenase mechanism. Appl. Environ. Microbiol. 71 (2005) 2473–2478. [DOI] [PMID: 15870336]
5.  Seidel, J., Schmitt, G., Hoffmann, M., Jendrossek, D. and Einsle, O. Structure of the processive rubber oxygenase RoxA from Xanthomonas sp. Proc. Natl. Acad. Sci. USA 110 (2013) 13833–13838. [DOI] [PMID: 23922395]
6.  Birke, J. and Jendrossek, D. Rubber oxygenase and latex clearing protein cleave rubber to different products and use different cleavage mechanisms. Appl. Environ. Microbiol. 80 (2014) 5012–5020. [DOI] [PMID: 24907333]
7.  Birke, J., Röther, W. and Jendrossek, D. RoxB is a novel type of rubber oxygenase that combines properties of rubber oxygenase RoxA and latex clearing protein (Lcp). Appl. Environ. Microbiol. 83 (2017) e00721-17. [PMID: 28500046]
[EC 1.13.11.87 created 2018]
 
 
EC 1.14.13.69     
Accepted name: alkene monooxygenase
Reaction: propene + NADH + H+ + O2 = 1,2-epoxypropane + NAD+ + H2O
For diagram of epoxide carboxylation, click here and for diagram of isoprene biosynthesis and metabolism, click here
Other name(s): alkene epoxygenase; etnABCD (gene names); amoABCDE (gene names)
Systematic name: alkene,NADH:oxygen oxidoreductase
Comments: This bacterial binuclear non-heme iron enzyme is a multicomponent enzyme complex comprising an oxygenase, a reductase, and a Rieske-type ferredoxin. The enzyme from the bacterium Xanthobacter sp. strain Py2 contains an additional small protein of unknown function that is essential for activity. In general, the enzyme oxygenates C2 to C6 aliphatic alkenes, although enzymes from different organisms show different substrate range. With propene as substrate, the stereospecificity of the epoxypropane formed is 95% (R) and 5% (S).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 63439-50-9
References:
1.  Small, F.J. and Ensign, S.A. Alkene monooxygenase from Xanthobacter strain Py2: purification and characterization of a four-component system central to the bacterial metabolism of aliphatic alkenes. J. Biol. Chem. 272 (1997) 24913–24920. [DOI] [PMID: 9312093]
2.  Gallagher, S.C., Cammack, R. and Dalton, H. Alkene monooxygenase from Nocardia corallina B-276 is a member of the class of dinuclear iron proteins capable of stereospecific epoxygenation reactions. Eur. J. Biochem. 247 (1997) 635–641. [DOI] [PMID: 9266707]
3.  Zhou, N.Y., Jenkins, A., Chion, C.K.N.C.K. and Leak, D.J. The alkene monooxygenase from Xanthobacter strain Py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. Appl. Environ. Microbiol. 65 (1999) 1589–1595. [PMID: 10103255]
4.  Champreda, V., Zhou, N.Y. and Leak, D.J. Heterologous expression of alkene monooxygenase components from Xanthobacter autotrophicus Py2 and reconstitution of the active complex. FEMS Microbiol. Lett. 239 (2004) 309–318. [DOI] [PMID: 15476981]
5.  Champreda, V., Choi, Y.J., Zhou, N.Y. and Leak, D.J. Alteration of the stereo- and regioselectivity of alkene monooxygenase based on coupling protein interactions. Appl. Microbiol. Biotechnol. 71 (2006) 840–847. [DOI] [PMID: 16402171]
[EC 1.14.13.69 created 2001]
 
 
EC 2.4.2.43     
Accepted name: lipid IVA 4-amino-4-deoxy-L-arabinosyltransferase
Reaction: (1) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + α-Kdo-(2→4)-α-Kdo-(2→6)-lipid A = α-Kdo-(2→4)-α-Kdo-(2→6)-[4-P-L-Ara4N]-lipid A + ditrans,octacis-undecaprenyl phosphate
(2) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + lipid IVA = lipid IIA + ditrans,octacis-undecaprenyl phosphate
(3) 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate + α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = 4′-α-L-Ara4N-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA + ditrans,octacis-undecaprenyl phosphate
For diagram of lipid IIA biosynthesis, click here
Glossary: lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
lipid IIA = 4-amino-4-deoxy-β-L-arabinopyranosyl 2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-α-D-glucopyranosyl phosphate
α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-hydroxytetradecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
4′-α-L-Ara4N-α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA = 4-amino-4-deoxy-α-L-arabinopyranosyl 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-phospho-β-D-glucopyranosy-(1→6)-2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-α-D-glucopyranosyl phosphate
lipid A = lipid A of Escherichia coli = 2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
α-Kdo-(2→4)-α-Kdo-(2→6)-lipid A = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
α-Kdo-(2→4)-α-Kdo-(2→6)-[4′-P-α-L-Ara4N]-lipid A = (3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→4)-(3-deoxy-α-D-manno-oct-2-ulopyranosylonate)-(2→6)-2-deoxy-2-{[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino}-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-(4-amino-4-deoxy-α-L-arabinopyranosyl)phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): undecaprenyl phosphate-α-L-Ara4N transferase; 4-amino-4-deoxy-L-arabinose lipid A transferase; polymyxin resistance protein PmrK; arnT (gene name)
Systematic name: 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl-phosphate:lipid IVA 4-amino-4-deoxy-L-arabinopyranosyltransferase
Comments: Integral membrane protein present in the inner membrane of certain Gram negative endobacteria. In strains that do not produce 3-deoxy-D-manno-octulosonic acid (Kdo), the enzyme adds a single arabinose unit to the 1-phosphate moiety of the tetra-acylated lipid A precursor, lipid IVA. In the presence of a Kdo disaccharide, the enzyme primarily adds an arabinose unit to the 4-phosphate of lipid A molecules. The Salmonella typhimurium enzyme can add arabinose units to both positions.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Trent, M.S., Ribeiro, A.A., Lin, S., Cotter, R.J. and Raetz, C.R. An inner membrane enzyme in Salmonella and Escherichia coli that transfers 4-amino-4-deoxy-L-arabinose to lipid A: induction on polymyxin-resistant mutants and role of a novel lipid-linked donor. J. Biol. Chem. 276 (2001) 43122–43131. [DOI] [PMID: 11535604]
2.  Trent, M.S., Ribeiro, A.A., Doerrler, W.T., Lin, S., Cotter, R.J. and Raetz, C.R. Accumulation of a polyisoprene-linked amino sugar in polymyxin-resistant Salmonella typhimurium and Escherichia coli: structural characterization and transfer to lipid A in the periplasm. J. Biol. Chem. 276 (2001) 43132–43144. [DOI] [PMID: 11535605]
3.  Zhou, Z., Ribeiro, A.A., Lin, S., Cotter, R.J., Miller, S.I. and Raetz, C.R. Lipid A modifications in polymyxin-resistant Salmonella typhimurium: PMRA-dependent 4-amino-4-deoxy-L-arabinose, and phosphoethanolamine incorporation. J. Biol. Chem. 276 (2001) 43111–43121. [DOI] [PMID: 11535603]
4.  Bretscher, L.E., Morrell, M.T., Funk, A.L. and Klug, C.S. Purification and characterization of the L-Ara4N transferase protein ArnT from Salmonella typhimurium. Protein Expr. Purif. 46 (2006) 33–39. [DOI] [PMID: 16226890]
5.  Impellitteri, N.A., Merten, J.A., Bretscher, L.E. and Klug, C.S. Identification of a functionally important loop in Salmonella typhimurium ArnT. Biochemistry 49 (2010) 29–35. [DOI] [PMID: 19947657]
[EC 2.4.2.43 created 2010, modified 2011]
 
 
EC 2.5.1.41     
Accepted name: phosphoglycerol geranylgeranyltransferase
Reaction: geranylgeranyl diphosphate + sn-glycerol 1-phosphate = diphosphate + 3-(O-geranylgeranyl)-sn-glycerol 1-phosphate
For diagram of archaetidylserine biosynthesis, click here
Glossary: sn-glycerol 1-phosphate = sn-glyceryl phosphate = (S)-2,3-dihydroxypropyl dihydrogen phosphate
Other name(s): glycerol phosphate geranylgeranyltransferase; geranylgeranyl-transferase (ambiguous); prenyltransferase (ambiguous); (S)-3-O-geranylgeranylglyceryl phosphate synthase; (S)-geranylgeranylglyceryl phosphate synthase; GGGP synthase; (S)-GGGP synthase; GGGPS; geranylgeranyl diphosphate:sn-glyceryl phosphate geranylgeranyltransferase; geranylgeranyl diphosphate:sn-glycerol-1-phosphate geranylgeranyltransferase
Systematic name: geranylgeranyl-diphosphate:sn-glycerol-1-phosphate geranylgeranyltransferase
Comments: This cytosolic enzyme catalyses the first pathway-specific step in the biosynthesis of the core membrane diether lipids in archaebacteria [2]. Requires Mg2+ for maximal activity [2]. It catalyses the alkylation of the primary hydroxy group in sn-glycerol 1-phosphate by geranylgeranyl diphosphate (GGPP) in a prenyltransfer reaction where a hydroxy group is the nucleophile in the acceptor substrate [2]. The other enzymes involved in the biosynthesis of polar lipids in Archaea are EC 1.1.1.261 (sn-glycerol-1-phosphate dehydrogenase), EC 2.5.1.42 (geranylgeranylglycerol-phosphate geranylgeranyltransferase) and EC 2.7.7.67 (CDP-archaeol synthase), which lead to the formation of CDP-unsaturated archaeol. The final step in the pathway involves the addition of L-serine, with concomitant removal of CMP, leading to the production of unsaturated archaetidylserine [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 124650-69-7
References:
1.  Zhang, D.-L., Daniels, L. and Poulter, C.D. Biosynthesis of archaebacterial membranes. Formation of isoprene ethers by a prenyl transfer reaction. J. Am. Chem. Soc. 112 (1990) 1264–1265.
2.  Chen, A., Zhang, D. and Poulter, C.D. (S)-Geranylgeranylglyceryl phosphate synthase. Purification and characterization of the first pathway-specific enzyme in archaebacterial membrane lipid biosynthesis. J. Biol. Chem. 268 (1993) 21701–21705. [PMID: 8408023]
3.  Nemoto, N., Oshima, T. and Yamagishi, A. Purification and characterization of geranylgeranylglyceryl phosphate synthase from a thermoacidophilic archaeon, Thermoplasma acidophilum. J. Biochem. 133 (2003) 651–657. [PMID: 12801917]
4.  Payandeh, J., Fujihashi, M., Gillon, W. and Pai, E.F. The crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase reveals an ancient fold for an ancient enzyme. J. Biol. Chem. 281 (2006) 6070–6078. [DOI] [PMID: 16377641]
5.  Morii, H., Nishihara, M. and Koga, Y. CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. J. Biol. Chem. 275 (2000) 36568–36574. [DOI] [PMID: 10960477]
[EC 2.5.1.41 created 1992, modified 2009]
 
 
EC 2.5.1.42     
Accepted name: geranylgeranylglycerol-phosphate geranylgeranyltransferase
Reaction: geranylgeranyl diphosphate + 3-(O-geranylgeranyl)-sn-glycerol 1-phosphate = diphosphate + 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate
For diagram of archaetidylserine biosynthesis, click here
Other name(s): geranylgeranyloxyglycerol phosphate geranylgeranyltransferase; geranylgeranyltransferase II; (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase; DGGGP synthase; DGGGPS; geranylgeranyl diphosphate:sn-3-O-(geranylgeranyl)glycerol 1-phosphate geranylgeranyltransferase
Systematic name: geranylgeranyl-diphosphate:3-(O-geranylgeranyl)-sn-glycerol 1-phosphate geranylgeranyltransferase
Comments: This enzyme is an integral-membrane protein that carries out the second prenyltransfer reaction involved in the formation of polar membrane lipids in Archaea. Requires a divalent metal cation, such as Mg2+ or Mn2+, for activity [2]. 4-Hydroxybenzoate, 1,4-dihydroxy 2-naphthoate, homogentisate and α-glycerophosphate cannot act as prenyl-acceptor substrates [2]. The other enzymes involved in the biosynthesis of polar lipids in Archaea are EC 1.1.1.261 (sn-glycerol-1-phosphate dehydrogenase), EC 2.5.1.41 (phosphoglycerol geranylgeranyltransferase), which, together with this enzyme, alkylates the hydroxy groups of glycerol 1-phosphate to yield unsaturated archaetidic acid, which is acted upon by EC 2.7.7.67 [CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol synthase] to form CDP-unsaturated archaeol. The final step in the pathway involves the addition of L-serine, with concomitant removal of CMP, leading to the production of unsaturated archaetidylserine [3]. Belongs in the UbiA prenyltransferase family [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 124650-68-6
References:
1.  Zhang, D.-L., Daniels, L. and Poulter, C.D. Biosynthesis of archaebacterial membranes. Formation of isoprene ethers by a prenyl transfer reaction. J. Am. Chem. Soc. 112 (1990) 1264–1265.
2.  Hemmi, H., Shibuya, K., Takahashi, Y., Nakayama, T. and Nishino, T. (S)-2,3-Di-O-geranylgeranylglyceryl phosphate synthase from the thermoacidophilic archaeon Sulfolobus solfataricus. Molecular cloning and characterization of a membrane-intrinsic prenyltransferase involved in the biosynthesis of archaeal ether-linked membrane lipids. J. Biol. Chem. 279 (2004) 50197–50203. [DOI] [PMID: 15356000]
3.  Morii, H., Nishihara, M. and Koga, Y. CTP:2,3-di-O-geranylgeranyl-sn-glycero-1-phosphate cytidyltransferase in the methanogenic archaeon Methanothermobacter thermoautotrophicus. J. Biol. Chem. 275 (2000) 36568–36574. [DOI] [PMID: 10960477]
[EC 2.5.1.42 created 1992, modified 2009]
 
 
EC 2.5.1.58     
Accepted name: protein farnesyltransferase
Reaction: farnesyl diphosphate + protein-cysteine = S-farnesyl protein + diphosphate
Other name(s): FTase
Systematic name: farnesyl-diphosphate:protein-cysteine farnesyltransferase
Comments: This enzyme, along with protein geranylgeranyltransferase types I (EC 2.5.1.59) and II (EC 2.5.1.60), constitutes the protein prenyltransferase family of enzymes. Catalyses the formation of a thioether linkage between the C-1 of an isoprenyl group and a cysteine residue fourth from the C-terminus of the protein. These protein acceptors have the C-terminal sequence CA1A2X, where the terminal residue, X, is preferably serine, methionine, alanine or glutamine; leucine makes the protein a substrate for EC 2.5.1.59. The enzymes are relaxed in specificity for A1, but cannot act if A2 is aromatic. Substrates of the prenyltransferases include Ras, Rho, Rab, other Ras-related small GTP-binding proteins, γ-subunits of heterotrimeric G-proteins, nuclear lamins, centromeric proteins and many proteins involved in visual signal transduction. A zinc metalloenzyme that requires Mg2+ for activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 131384-38-8
References:
1.  Furfine, E.S., Leban, J.J., Landavazo, A., Moomaw, J.F. and Casey, P.J. Protein farnesyltransferase: kinetics of farnesyl pyrophosphate binding and product release. Biochemistry 34 (1995) 6857–6862. [PMID: 7756316]
2.  Casey, P.J. and Seabra, M.C. Protein prenyltransferases. J. Biol. Chem. 271 (1996) 5289–5292. [DOI] [PMID: 8621375]
3.  Long, S.B., Casey, P.J. and Beese, L.S. Cocrystal structure of protein farnesyltransferase complexed with a farnesyl diphosphate substrate. Biochemistry 37 (1998) 9612–9618. [DOI] [PMID: 9657673]
4.  Micali, E., Chehade, K.A., Isaacs, R.J., Andres, D.A. and Spielmann, H.P. Protein farnesyltransferase isoprenoid substrate discrimination is dependent on isoprene double bonds and branched methyl groups. Biochemistry 40 (2001) 12254–12265. [DOI] [PMID: 11591144]
5.  Long, S.B., Casey, P.J. and Beese, L.S. Reaction path of protein farnesyltransferase at atomic resolution. Nature 419 (2002) 645–650. [DOI] [PMID: 12374986]
6.  Gibbs, R.A. Prenyl transfer and the enzymes of terpenoid and steroid biosynthesis. In: Sinnott, M. (Ed.), Comprehensive Biological Catalysis. A Mechanistic Reference, vol. 1, Academic Press, San Diego, CA, 1998, pp. 31–118.
[EC 2.5.1.58 created 2003]
 
 
EC 2.5.1.67     
Accepted name: chrysanthemyl diphosphate synthase
Reaction: 2 prenyl diphosphate = diphosphate + chrysanthemyl diphosphate
For diagram of reaction, click here
Glossary: chrysanthemyl = [2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropyl]methyl
chrysanthemic acid = 2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropane-1-carboxylic acid
Other name(s): CPPase; dimethylallyl-diphosphate:dimethylallyl-diphosphate dimethylallyltransferase (chrysanthemyl-diphosphate-forming)
Systematic name: prenyl-diphosphate:prenyl-diphosphate prenyltransferase (chrysanthemyl-diphosphate-forming)
Comments: Requires a divalent metal ion for activity, with Mg2+ being better than Mn2+ [1]. Chrysanthemyl diphosphate is a monoterpene with a non-head-to-tail linkage. It is unlike most monoterpenoids, which are derived from geranyl diphosphate and have isoprene units that are linked head-to-tail. The mechanism of its formation is similar to that of the early steps of squalene and phytoene biosynthesis. Chrysanthemyl diphosphate is the precursor of chrysanthemic acid, the acid half of the pyrethroid insecticides found in chrysanthemums.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Rivera, S.B., Swedlund, B.D., King, G.J., Bell, R.N., Hussey, C.E., Jr., Shattuck-Eidens, D.M., Wrobel, W.M., Peiser, G.D. and Poulter, C.D. Chrysanthemyl diphosphate synthase: isolation of the gene and characterization of the recombinant non-head-to-tail monoterpene synthase from Chrysanthemum cinerariaefolium. Proc. Natl. Acad. Sci. USA 98 (2001) 4373–4378. [DOI] [PMID: 11287653]
2.  Erickson, H.K. and Poulter, C.D. Chrysanthemyl diphosphate synthase. The relationship among chain elongation, branching, and cyclopropanation reactions in the isoprenoid biosynthetic pathway. J. Am. Chem. Soc. 125 (2003) 6886–6888. [DOI] [PMID: 12783539]
[EC 2.5.1.67 created 2007]
 
 
EC 2.5.1.69     
Accepted name: lavandulyl diphosphate synthase
Reaction: 2 prenyl diphosphate = diphosphate + lavandulyl diphosphate
For diagram of reaction, click here
Glossary: lavandulyl = 5-methyl-2-(prop-1-en-2-yl)hex-4-en-1-yl
Other name(s): FDS-5; dimethylallyl-diphosphate:dimethylallyl-diphosphate dimethylallyltransferase (lavandulyl-diphosphate-forming)
Systematic name: prenyl-diphosphate:prenyl-diphosphate prenyltransferase (lavandulyl-diphosphate-forming)
Comments: Lavandulyl diphosphate is a monoterpene with a non-head-to-tail linkage. It is unlike most monoterpenoids, which are derived from geranyl diphosphate and have isoprene units that are linked head-to-tail. When this enzyme is incubated with prenyl diphosphate and 3-methylbut-3-en-1-yl diphosphate, it also forms the regular monoterpene geranyl diphosphate [2]. The enzyme from Artemisia tridentata (big sagebrush) forms both lavandulyl diphosphate and chrysanthemyl diphosphate (see EC 2.5.1.67, chrysanthemyl diphosphate synthase) when prenyl diphosphate is the sole substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Erickson, H.K. and Poulter, C.D. Chrysanthemyl diphosphate synthase. The relationship among chain elongation, branching, and cyclopropanation reactions in the isoprenoid biosynthetic pathway. J. Am. Chem. Soc. 125 (2003) 6886–6888. [DOI] [PMID: 12783539]
2.  Hemmerlin, A., Rivera, S.B., Erickson, H.K. and Poulter, C.D. Enzymes encoded by the farnesyl diphosphate synthase gene family in the Big Sagebrush Artemisia tridentata ssp. spiciformis. J. Biol. Chem. 278 (2003) 32132–32140. [DOI] [PMID: 12782626]
[EC 2.5.1.69 created 2007]
 
 
EC 2.5.1.87     
Accepted name: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10–55)
For diagram of di- and tritrans,polycis-polyprenol biosynthesis, click here
Other name(s): RER2; Rer2p; Rer2p Z-prenyltransferase; Srt1p; Srt2p Z-prenyltransferase; ACPT; dehydrodolichyl diphosphate synthase 1
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 10–55 isopentenyl units)
Comments: The enzyme is involved in biosynthesis of dolichol (a long-chain polyprenol) with a saturated α-isoprene unit, which serves as a glycosyl carrier in protein glycosylation [1]. The yeast Saccharomyces cerevisiae has two different enzymes that catalyse this reaction. Rer2p synthesizes a well-defined family of polyprenols of 13–18 isoprene residues with dominating C80 (16 isoprene residues) extending to C120, while Srt1p synthesizes mainly polyprenol with 22 isoprene subunits. Largest Srt1p products reach C290 [2]. The enzyme from Arabidopsis thaliana catalyses the formation of polyprenyl diphosphates with predominant carbon number C120 [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sato, M., Fujisaki, S., Sato, K., Nishimura, Y. and Nakano, A. Yeast Saccharomyces cerevisiae has two cis-prenyltransferases with different properties and localizations. Implication for their distinct physiological roles in dolichol synthesis. Genes Cells 6 (2001) 495–506. [DOI] [PMID: 11442630]
2.  Poznanski, J. and Szkopinska, A. Precise bacterial polyprenol length control fails in Saccharomyces cerevisiae. Biopolymers 86 (2007) 155–164. [DOI] [PMID: 17345630]
3.  Sato, M., Sato, K., Nishikawa, S., Hirata, A., Kato, J. and Nakano, A. The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis. Mol. Cell Biol. 19 (1999) 471–483. [DOI] [PMID: 9858571]
4.  Oh, S.K., Han, K.H., Ryu, S.B. and Kang, H. Molecular cloning, expression, and functional analysis of a cis-prenyltransferase from Arabidopsis thaliana. Implications in rubber biosynthesis. J. Biol. Chem. 275 (2000) 18482–18488. [DOI] [PMID: 10764783]
5.  Cunillera, N., Arro, M., Fores, O., Manzano, D. and Ferrer, A. Characterization of dehydrodolichyl diphosphate synthase of Arabidopsis thaliana, a key enzyme in dolichol biosynthesis. FEBS Lett. 477 (2000) 170–174. [DOI] [PMID: 10908715]
[EC 2.5.1.87 created 2010]
 
 
EC 2.5.1.149     
Accepted name: lycopene elongase/hydratase (flavuxanthin-forming)
Reaction: (1) prenyl diphosphate + all-trans-lycopene + acceptor + H2O = nonaflavuxanthin + reduced electron acceptor + diphosphate
(2) prenyl diphosphate + nonaflavuxanthin + acceptor + H2O = flavuxanthin + reduced electron acceptor + diphosphate
Glossary: flavuxanthin = 2,2′-bis-(4-hydroxy-3-methylbut-2-enyl)-1,16,1′,16′-tetradehydro-1,2,1′,2′-tetrahydro-ψ,ψ-carotene = (2E,8E,10E,12E,14E,16E,18E,20E,22E,24E,26E,28E,34E)-5,32-diisopropenyl-2,8,12,16,21,25,29,35-octamethylhexatriaconta-2,8,10,12,14,16,18,20,22,24,26,28,34-tridecaene-1,36-diol
Other name(s): crtEb (gene name); dimethylallyl-diphosphate:all-trans-lycopene dimethylallyltransferase (hydrating, flavuxanthin-forming)
Systematic name: prenyl-diphosphate:all-trans-lycopene prenyltransferase (hydrating, flavuxanthin-forming)
Comments: The enzyme, characterized from the bacterium Corynebacterium glutamicum, is bifunctional. It catalyses the elongation of the C40 carotenoid all-trans-lycopene by attaching an isoprene unit at C-2, as well as the hydroxylation of the new isoprene unit. The enzyme acts at both ends of the substrate, forming the C50 carotenoid flavuxanthin via the C45 intermediate nonaflavuxanthin. cf. EC 2.5.1.150, lycopene elongase/hydratase (dihydrobisanhydrobacterioruberin-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Krubasik, P., Kobayashi, M. and Sandmann, G. Expression and functional analysis of a gene cluster involved in the synthesis of decaprenoxanthin reveals the mechanisms for C50 carotenoid formation. Eur. J. Biochem. 268 (2001) 3702–3708. [PMID: 11432736]
2.  Heider, S.A., Peters-Wendisch, P. and Wendisch, V.F. Carotenoid biosynthesis and overproduction in Corynebacterium glutamicum. BMC Microbiol. 12:198 (2012). [PMID: 22963379]
[EC 2.5.1.149 created 2018]
 
 
EC 2.5.1.150     
Accepted name: lycopene elongase/hydratase (dihydrobisanhydrobacterioruberin-forming)
Reaction: (1) prenyl diphosphate + all-trans-lycopene + H2O = dihydroisopentenyldehydrorhodopin + diphosphate
(2) prenyl diphosphate + isopentenyldehydrorhodopin + H2O = dihydrobisanhydrobacterioruberin + diphosphate
Glossary: dihydrobisanhydrobacterioruberin = (2S,2S′)-2,2′-bis(3-methylbut-2-en-1-yl)-3,3′,4,4′-tetradehydro-1,1′,2,2′-tetrahydro-ψ,ψ-carotene-1,1′-diol = (3S,4E,6E,8E,10E,12E,14E,16E,18E,20E,22E,24E,26E,30R)-2,6,10,14,19,23,27,31-octamethyl-3,30-bis(3-methylbut-2-en-1-yl)dotriaconta-4,6,8,10,12,14,16,18,20,22,24,26-dodecaene-2,31-diol
Other name(s): lbtA (gene name); lyeJ (gene name); dimethylallyl-diphosphate:all-trans-lycopene dimethylallyltransferase (hydrating, dihydrobisanhydrobacterioruberin-forming)
Systematic name: prenyl-diphosphate:all-trans-lycopene prenyltransferase (hydrating, dihydrobisanhydrobacterioruberin-forming)
Comments: The enzyme, characterized from the bacterium Dietzia sp. CQ4 and the halophilic archaea Halobacterium salinarum and Haloarcula japonica, is bifunctional. It catalyses the elongation of the C40 carotenoid all-trans-lycopene by attaching an isoprene unit at C-2 as well as the hydroxylation of the previous end of the molecule. The enzyme acts at both ends of the substrate, and combined with the action of EC 1.3.99.37, 1-hydroxy-2-isopentenylcarotenoid 3,4-desaturase, it forms the C50 carotenoid dihydrobisanhydrobacterioruberin. cf. EC 2.5.1.149, lycopene elongase/hydratase (flavuxanthin-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Tao, L., Yao, H. and Cheng, Q. Genes from a Dietzia sp. for synthesis of C40 and C50 β-cyclic carotenoids. Gene 386 (2007) 90–97. [DOI] [PMID: 17008032]
2.  Dummer, A.M., Bonsall, J.C., Cihla, J.B., Lawry, S.M., Johnson, G.C. and Peck, R.F. Bacterioopsin-mediated regulation of bacterioruberin biosynthesis in Halobacterium salinarum. J. Bacteriol. 193 (2011) 5658–5667. [PMID: 21840984]
3.  Yang, Y., Yatsunami, R., Ando, A., Miyoko, N., Fukui, T., Takaichi, S. and Nakamura, S. Complete biosynthetic pathway of the C50 carotenoid bacterioruberin from lycopene in the extremely halophilic archaeon Haloarcula japonica. J. Bacteriol. 197 (2015) 1614–1623. [DOI] [PMID: 25712483]
[EC 2.5.1.150 created 2018]
 
 
EC 4.2.3.27     
Accepted name: isoprene synthase
Reaction: prenyl diphosphate = isoprene + diphosphate
For diagram of isoprene biosynthesis and metabolism, click here
Glossary: isoprene = 2-methylbuta-1,3-diene
Other name(s): ISPC; ISPS; dimethylallyl-diphosphate diphosphate-lyase (isoprene-forming)
Systematic name: prenyl-diphosphate diphosphate-lyase (isoprene-forming)
Comments: Requires Mg2+ or Mn2+ for activity. This enzyme is located in the chloroplast of isoprene-emitting plants, such as poplar and aspen, and may be activitated by light-dependent changes in chloroplast pH and Mg2+ concentration [2,8].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 139172-14-8
References:
1.  Silver, G.M. and Fall, R. Enzymatic synthesis of isoprene from dimethylallyl diphosphate in aspen leaf extracts. Plant Physiol. 97 (1991) 1588–1591. [PMID: 16668590]
2.  Silver, G.M. and Fall, R. Characterization of aspen isoprene synthase, an enzyme responsible for leaf isoprene emission to the atmosphere. J. Biol. Chem. 270 (1995) 13010–13016. [DOI] [PMID: 7768893]
3.  Wildermuth, M.C. and Fall, R. Light-dependent isoprene emission (characterization of a thylakoid-bound isoprene synthase in Salix discolor chloroplasts). Plant Physiol. 112 (1996) 171–182. [PMID: 12226383]
4.  Schnitzler, J.P., Arenz, R., Steinbrecher, R. and Lehming, A. Characterization of an isoprene synthase from leaves of Quercus petraea. Bot. Acta 109 (1996) 216–221.
5.  Miller, B., Oschinski, C. and Zimmer, W. First isolation of an isoprene synthase gene from poplar and successful expression of the gene in Escherichia coli. Planta 213 (2001) 483–487. [PMID: 11506373]
6.  Sivy, T.L., Shirk, M.C. and Fall, R. Isoprene synthase activity parallels fluctuations of isoprene release during growth of Bacillus subtilis. Biochem. Biophys. Res. Commun. 294 (2002) 71–75. [DOI] [PMID: 12054742]
7.  Sasaki, K., Ohara, K. and Yazaki, K. Gene expression and characterization of isoprene synthase from Populus alba. FEBS Lett. 579 (2005) 2514–2518. [DOI] [PMID: 15848197]
8.  Schnitzler, J.-P., Zimmer, I., Bachl, A., Arend, M., Fromm, J. and Fischbach, R.J. Biochemical properties of isoprene synthase in poplar (Populus x canescens). Planta 222 (2005) 777–786. [DOI] [PMID: 16052321]
[EC 4.2.3.27 created 2007]
 
 
EC 4.4.1.34     
Accepted name: isoprene-epoxide—glutathione S-transferase
Reaction: 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol = (3R)-3,4-epoxy-3-methylbut-1-ene + glutathione
For diagram of isoprene biosynthesis and metabolism, click here
Other name(s): isoI (gene name)
Systematic name: 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol lyase [(3R)-3,4-epoxy-3-methylbut-1-ene-forming]
Comments: The enzyme, characterized from the bacterium Rhodococcus sp. AD45, is involved in isoprene degradation. The enzyme can catalyse the glutathione-dependent ring opening of various epoxides, but the highest activity is with (3R)-3,4-epoxy-3-methylbut-1-ene, which is derived from isoprene by EC 1.14.13.69, alkene monooxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  van Hylckama Vlieg, J.E., Kingma, J., van den Wijngaard, A.J. and Janssen, D.B. A glutathione S-transferase with activity towards cis-1, 2-dichloroepoxyethane is involved in isoprene utilization by Rhodococcus sp. strain AD45. Appl. Environ. Microbiol. 64 (1998) 2800–2805. [PMID: 9687433]
2.  van Hylckama Vlieg, J.E., Kingma, J., Kruizinga, W. and Janssen, D.B. Purification of a glutathione S-transferase and a glutathione conjugate-specific dehydrogenase involved in isoprene metabolism in Rhodococcus sp. strain AD45. J. Bacteriol. 181 (1999) 2094–2101. [PMID: 10094686]
[EC 4.4.1.34 created 2016]
 
 


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