The Enzyme Database

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EC 1.3.1.83     
Accepted name: geranylgeranyl diphosphate reductase
Reaction: phytyl diphosphate + 3 NADP+ = geranylgeranyl diphosphate + 3 NADPH + 3 H+
For diagram of acyclic diterpenoid biosynthesis, click here
Other name(s): geranylgeranyl reductase; CHL P
Systematic name: geranylgeranyl-diphosphate:NADP+ oxidoreductase
Comments: This enzyme also acts on geranylgeranyl-chlorophyll a. The reaction occurs in three steps. Which order the three double bonds are reduced is not known.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Soll, J., Schultz, G., Rudiger, W. and Benz, J. Hydrogenation of geranylgeraniol : two pathways exist in spinach chloroplasts. Plant Physiol. 71 (1983) 849–854. [PMID: 16662918]
2.  Tanaka, R., Oster, U., Kruse, E., Rudiger, W. and Grimm, B. Reduced activity of geranylgeranyl reductase leads to loss of chlorophyll and tocopherol and to partially geranylgeranylated chlorophyll in transgenic tobacco plants expressing antisense RNA for geranylgeranyl reductas. Plant Physiol. 120 (1999) 695–704. [PMID: 10398704]
3.  Keller, Y., Bouvier, F., d'Harlingue, A. and Camara, B. Metabolic compartmentation of plastid prenyllipid biosynthesis—evidence for the involvement of a multifunctional geranylgeranyl reductase. Eur. J. Biochem. 251 (1998) 413–417. [PMID: 9492312]
[EC 1.3.1.83 created 2009]
 
 
EC 1.3.7.11     
Accepted name: 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase
Reaction: a 2,3-bis-(O-phytanyl)-sn-glycero-phospholipid + 16 oxidized ferredoxin [iron-sulfur] cluster = a 2,3-bis-(O-geranylgeranyl)-sn-glycero-phospholipid + 16 reduced ferredoxin [iron-sulfur] cluster + 16 H+
For diagram of archaetidylserine biosynthesis, click here
Glossary: phytanol = 3,7,11,15-tetramethylhexadecan-1-ol
Other name(s): AF0464 (gene name); 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor)
Systematic name: 2,3-bis-(O-phytanyl)-sn-glycero-phospholipid:ferredoxin oxidoreductase
Comments: A flavoprotein (FAD). The enzyme is involved in the biosynthesis of archaeal membrane lipids. It catalyses the reduction of all 8 double bonds in 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipids and all 4 double bonds in 3-O-geranylgeranyl-sn-glycerol phospholipids with comparable activity. Unlike EC 1.3.1.101, 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H], this enzyme shows no activity with NADPH, and requires a dedicated ferredoxin [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Murakami, M., Shibuya, K., Nakayama, T., Nishino, T., Yoshimura, T. and Hemmi, H. Geranylgeranyl reductase involved in the biosynthesis of archaeal membrane lipids in the hyperthermophilic archaeon Archaeoglobus fulgidus. FEBS J. 274 (2007) 805–814. [DOI] [PMID: 17288560]
2.  Sato, S., Murakami, M., Yoshimura, T. and Hemmi, H. Specific partial reduction of geranylgeranyl diphosphate by an enzyme from the thermoacidophilic archaeon Sulfolobus acidocaldarius yields a reactive prenyl donor, not a dead-end product. J. Bacteriol. 190 (2008) 3923–3929. [DOI] [PMID: 18375567]
3.  Sasaki, D., Fujihashi, M., Iwata, Y., Murakami, M., Yoshimura, T., Hemmi, H. and Miki, K. Structure and mutation analysis of archaeal geranylgeranyl reductase. J. Mol. Biol. 409 (2011) 543–557. [DOI] [PMID: 21515284]
4.  Isobe, K., Ogawa, T., Hirose, K., Yokoi, T., Yoshimura, T. and Hemmi, H. Geranylgeranyl reductase and ferredoxin from Methanosarcina acetivorans are required for the synthesis of fully reduced archaeal membrane lipid in Escherichia coli cells. J. Bacteriol. 196 (2014) 417–423. [DOI] [PMID: 24214941]
[EC 1.3.7.11 created 2013 as EC 1.3.99.34, transferred 2015 to EC 1.3.7.11 ]
 
 
EC 1.3.99.34      
Transferred entry: 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor). Now classified as EC 1.3.7.11, 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase.
[EC 1.3.99.34 created 2013, deleted 2015]
 
 
EC 2.1.1.255     
Accepted name: geranyl diphosphate 2-C-methyltransferase
Reaction: S-adenosyl-L-methionine + geranyl diphosphate = S-adenosyl-L-homocysteine + (E)-2-methylgeranyl diphosphate
For diagram of reaction, click here
Other name(s): SCO7701; GPP methyltransferase; GPPMT; 2-methyl-GPP synthase; MGPPS; geranyl pyrophosphate methyltransferase
Systematic name: S-adenosyl-L-methionine:geranyl-diphosphate 2-C-methyltransferase
Comments: This enzyme, along with EC 4.2.3.118, 2-methylisoborneol synthase, produces 2-methylisoborneol, an odiferous compound produced by soil microorganisms with a strong earthy/musty odour.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Wang, C.M. and Cane, D.E. Biochemistry and molecular genetics of the biosynthesis of the earthy odorant methylisoborneol in Streptomyces coelicolor. J. Am. Chem. Soc. 130 (2008) 8908–8909. [DOI] [PMID: 18563898]
2.  Ariyawutthiphan, O., Ose, T., Tsuda, M., Gao, Y., Yao, M., Minami, A., Oikawa, H. and Tanaka, I. Crystallization and preliminary X-ray crystallographic study of a methyltransferase involved in 2-methylisoborneol biosynthesis in Streptomyces lasaliensis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67 (2011) 417–420. [DOI] [PMID: 21393856]
3.  Komatsu, M., Tsuda, M., Omura, S., Oikawa, H. and Ikeda, H. Identification and functional analysis of genes controlling biosynthesis of 2-methylisoborneol. Proc. Natl. Acad. Sci. USA 105 (2008) 7422–7427. [DOI] [PMID: 18492804]
4.  Giglio, S., Chou, W.K., Ikeda, H., Cane, D.E. and Monis, P.T. Biosynthesis of 2-methylisoborneol in cyanobacteria. Environ. Sci. Technol. 45 (2011) 992–998. [DOI] [PMID: 21174459]
[EC 2.1.1.255 created 2012]
 
 
EC 2.5.1.1     
Accepted name: dimethylallyltranstransferase
Reaction: prenyl diphosphate + 3-methylbut-3-en-1-yl diphosphate = diphosphate + geranyl diphosphate
For diagram of terpenoid biosynthesis, click here
Glossary: 3-methylbut-3-en-1-yl = isopentenyl (ambiguous)
prenyl = 3-methylbut-2-en-1-yl = dimethylallyl (ambiguous)
Other name(s): geranyl-diphosphate synthase; prenyltransferase; dimethylallyltransferase; DMAPP:IPP-dimethylallyltransferase; (2E,6E)-farnesyl diphosphate synthetase; diprenyltransferase; geranyl pyrophosphate synthase; geranyl pyrophosphate synthetase; trans-farnesyl pyrophosphate synthetase; dimethylallyl-diphosphate:isopentenyl-diphosphate dimethylallyltranstransferase
Systematic name: prenyl-diphosphate:3-methylbut-3-en-1-yl-diphosphate prenyltranstransferase
Comments: This enzyme will not accept larger prenyl diphosphates as efficient donors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9032-79-5
References:
1.  Banthorpe, D.V., Bucknall, G.A., Doonan, H.J., Doonan, S. and Rowan, M.G. Biosynthesis of geraniol and nerol in cell-free extracts of Tanacetum vulgare. Phytochemistry 15 (1976) 91–100.
2.  Sagami, H., Ogura, K., Seto, S. and Kurokawa, T. A new prenyltransferase from Micrococcus lysodeikticus. Biochem. Biophys. Res. Commun. 85 (1978) 572–578. [DOI] [PMID: 736921]
[EC 2.5.1.1 created 1961]
 
 
EC 2.5.1.10     
Accepted name: (2E,6E)-farnesyl diphosphate synthase
Reaction: geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): farnesyl-diphosphate synthase; geranyl transferase I; prenyltransferase; farnesyl pyrophosphate synthetase; farnesylpyrophosphate synthetase; geranyltranstransferase
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate geranyltranstransferase
Comments: Some forms of this enzyme will also use dimethylallyl diphosphate as a substrate. The enzyme will not accept larger prenyl diphosphates as efficient donors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37277-79-5
References:
1.  Lynen, F., Agranoff, B.W., Eggerer, H., Henning, V. and Möslein, E.M. Zur Biosynthese der Terpene. VI. γ,γ-Dimethyl-allyl-pyrophosphat und Geranyl-pyrophosphat, biologische Vorstufen des Squalens. Angew. Chem. 71 (1959) 657–663.
2.  Ogura, K., Nishino, T. and Seto, S. The purification of prenyltransferase and isopentenyl pyrophosphate isomerase of pumpkin fruit and their some properties. J. Biochem. (Tokyo) 64 (1968) 197–203. [PMID: 4303505]
3.  Reed, B.C. and Rilling, H. Crystallization and partial characterization of prenyltransferase from avian liver. Biochemistry 14 (1975) 50–54. [PMID: 1109590]
4.  Takahashi, I. and Ogura, K. Farnesyl pyrophosphate synthetase from Bacillus subtilis. J. Biochem. (Tokyo) 89 (1981) 1581–1587. [PMID: 6792191]
5.  Takahashi, I. and Ogura, K. Prenyltransferases of Bacillus subtilis: undecaprenyl pyrophosphate synthetase and geranylgeranyl pyrophosphate synthetase. J. Biochem. (Tokyo) 92 (1982) 1527–1537. [PMID: 6818223]
[EC 2.5.1.10 created 1972, modified 2010]
 
 
EC 2.5.1.11      
Transferred entry: trans-octaprenyltranstransferase. Now covered by EC 2.5.1.84 (all-trans-nonaprenyl-diphosphate synthase [geranyl-diphosphate specific]) and EC 2.5.1.85 (all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific])
[EC 2.5.1.11 created 1972, deleted 2010]
 
 
EC 2.5.1.29     
Accepted name: geranylgeranyl diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): geranylgeranyl-diphosphate synthase; geranylgeranyl pyrophosphate synthetase; geranylgeranyl-PP synthetase; farnesyltransferase; geranylgeranyl pyrophosphate synthase; farnesyltranstransferase (obsolete)
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase
Comments: Some forms of this enzyme will also use geranyl diphosphate and dimethylallyl diphosphate as donors; it will not use larger prenyl diphosphates as efficient donors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9032-58-0
References:
1.  Sagami, H., Ishi, K. and Ogura, K. Occurrence and unusual properties of geranylgeranyl pyrophosphate synthetase of pig liver. Biochem. Int. 3 (1981) 669–675.
[EC 2.5.1.29 created 1984, modified 2011]
 
 
EC 2.5.1.32     
Accepted name: 15-cis-phytoene synthase
Reaction: 2 geranylgeranyl diphosphate = 15-cis-phytoene + 2 diphosphate (overall reaction)
(1a) 2 geranylgeranyl diphosphate = diphosphate + prephytoene diphosphate
(1b) prephytoene diphosphate = 15-cis-phytoene + diphosphate
For diagram of squalene, phytoene and 4,4′-diapophytoene biosynthesis, click here
Other name(s): PSY (gene name); crtB (gene name); prephytoene-diphosphate synthase; phytoene synthetase; PSase; geranylgeranyl-diphosphate geranylgeranyltransferase
Systematic name: geranylgeranyl-diphosphate:geranylgeranyl-diphosphate geranylgeranyltransferase (15-cis-phytoene-forming)
Comments: Requires Mn2+ for activity. The enzyme condenses two molecules of geranylgeranyl diphosphate to give prephytoene diphosphate, followed by rearrangement of the cyclopropylcarbinyl intermediate to 15-cis-phytoene.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 50936-61-3
References:
1.  Chamovitz, D., Misawa, N., Sandmann, G. and Hirschberg, J. Molecular cloning and expression in Escherichia coli of a cyanobacterial gene coding for phytoene synthase, a carotenoid biosynthesis enzyme. FEBS Lett. 296 (1992) 305–310. [DOI] [PMID: 1537409]
2.  Sandmann, G. and Misawa, N. New functional assignment of the carotenogenic genes crtB and crtE with constructs of these genes from Erwinia species. FEMS Microbiol. Lett. 69 (1992) 253–257. [PMID: 1555761]
3.  Scolnik, P.A. and Bartley, G.E. Nucleotide sequence of an Arabidopsis cDNA for phytoene synthase. Plant Physiol. 104 (1994) 1471–1472. [PMID: 8016277]
4.  Misawa, N., Truesdale, M.R., Sandmann, G., Fraser, P.D., Bird, C., Schuch, W. and Bramley, P.M. Expression of a tomato cDNA coding for phytoene synthase in Escherichia coli, phytoene formation in vivo and in vitro, and functional analysis of the various truncated gene products. J. Biochem. (Tokyo) 116 (1994) 980–985. [PMID: 7896759]
5.  Schledz, M., al-Babili, S., von Lintig, J., Haubruck, H., Rabbani, S., Kleinig, H. and Beyer, P. Phytoene synthase from Narcissus pseudonarcissus: functional expression, galactolipid requirement, topological distribution in chromoplasts and induction during flowering. Plant J. 10 (1996) 781–792. [DOI] [PMID: 8953242]
[EC 2.5.1.32 created 1984, modified 2005, modified 2012]
 
 
EC 2.5.1.33      
Transferred entry: trans-pentaprenyltranstransferase. Now covered by EC 2.5.1.82 (hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]) and EC 2.5.1.83 (hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific])
[EC 2.5.1.33 created 1984, deleted 2010]
 
 
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, PDB, 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, PDB, 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 2.5.1.59     
Accepted name: protein geranylgeranyltransferase type I
Reaction: geranylgeranyl diphosphate + protein-cysteine = S-geranylgeranyl-protein + diphosphate
Other name(s): GGTase-I; GGTaseI
Systematic name: geranylgeranyl-diphosphate:protein-cysteine geranyltransferase
Comments: This enzyme, along with protein farnesyltransferase (EC 2.5.1.58) and protein geranylgeranyltransferase type II (EC 2.5.1.60), constitutes the protein prenyltransferase family of enzymes. Catalyses the formation of a thioether linkage between the C-1 atom of the geranylgeranyl 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 leucine; serine, methionine, alanine or glutamine makes the protein a substrate for EC 2.5.1.58. The enzymes are relaxed in specificity for A1, but cannot act if A2 is aromatic. Known targets of this enzyme include most γ-subunits of heterotrimeric G proteins and Ras-related GTPases such as members of the Ras and Rac/Rho families. A zinc metalloenzyme. The Zn2+ is required for peptide, but not for isoprenoid, substrate binding.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 135371-29-8
References:
1.  Casey, P.J. and Seabra, M.C. Protein prenyltransferases. J. Biol. Chem. 271 (1996) 5289–5292. [DOI] [PMID: 8621375]
2.  Zhang, F.L. and Casey, P.J. Influence of metal ions on substrate binding and catalytic activity of mammalian protein geranylgeranyltransferase type-I. Biochem. J. 320 (1996) 925–932. [PMID: 9003382]
3.  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 2.5.1.59 created 2003]
 
 
EC 2.5.1.60     
Accepted name: protein geranylgeranyltransferase type II
Reaction: geranylgeranyl diphosphate + protein-cysteine = S-geranylgeranyl-protein + diphosphate
Other name(s): GGTaseII; Rab geranylgeranyltransferase; RabGGTase; geranylgeranyl-diphosphate,geranylgeranyl-diphosphate:protein-cysteine geranyltransferase
Systematic name: geranylgeranyl-diphosphate:protein-cysteine geranyltransferase
Comments: This enzyme, along with protein farnesyltransferase (EC 2.5.1.58) and protein geranylgeranyltransferase type I (EC 2.5.1.59), constitutes the protein prenyltransferase family of enzymes. Attaches geranylgeranyl groups to two C-terminal cysteines in Ras-related GTPases of a single family, the Rab family (Ypt/Sec4 in lower eukaryotes) that terminate in XXCC, XCXC and CCXX motifs. Reaction is entirely dependent on the Rab substrate being bound to Rab escort protein (REP). Post-translational modification with the geranylgeranyl moiety is essential for Rab GTPases to be able to control the processes of membrane docking and fusion [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 135371-29-8
References:
1.  Casey, P.J. and Seabra, M.C. Protein prenyltransferases. J. Biol. Chem. 271 (1996) 5289–5292. [DOI] [PMID: 8621375]
2.  Wilson, A.L., Erdman, R.A., Castellano, F. and Maltese, W.A. Prenylation of Rab8 GTPase by type I and type II geranylgeranyl transferases. Biochem. J. 333 (1998) 497–504. [PMID: 9677305]
3.  Zhang, H., Seabra, M.C. and Deisenhofer, J. Crystal structure of Rab geranylgeranyltransferase at 2.0 Å resolution. Structure 8 (2000) 241–251. [PMID: 10745007]
4.  Thomä, N.H., Niculae, A., Goody, R.S. and Alexandrov, K. Double prenylation by RabGGTase can proceed without dissociation of the mono-prenylated intermediate. J. Biol. Chem. 276 (2001) 48631–48636. [DOI] [PMID: 11591706]
5.  Rak, A., Niculae, A., Kalinin, A., Thomä, N.H., Sidorovitch, V., Goody, R.S. and Alexandrov, K. In vitro assembly, purification, and crystallization of the Rab geranylgeranyl transferase:substrate complex. Protein Expr. Purif. 25 (2002) 23–30. [DOI] [PMID: 12071695]
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 2.5.1.60 created 2003]
 
 
EC 2.5.1.62     
Accepted name: chlorophyll synthase
Reaction: chlorophyllide a + phytyl diphosphate = chlorophyll a + diphosphate
For diagram of the later stages of chlorophyll biosynthesis, click here
Systematic name: chlorophyllide-a:phytyl-diphosphate phytyltransferase
Comments: Requires Mg2+. The enzyme is modified by binding of the first substrate, phytyl diphosphate, before reaction of the modified enzyme with the second substrate, chlorophyllide a, can occur. The reaction also occurs when phytyl diphosphate is replaced by geranylgeranyl diphosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9077-08-1
References:
1.  Schmid, H.C., Rassadina, V., Oster, U., Schoch, S. and Rüdiger, W. Pre-loading of chlorophyll synthase with tetraprenyl diphosphate is an obligatory step in chlorophyll biosynthesis. Biol. Chem. 383 (2002) 1769–1778. [DOI] [PMID: 12530542]
2.  Oster, U., Bauer, C.E. and Rüdiger, W. Characterization of chlorophyll a and bacteriochlorophyll a synthases by heterologous expression in Escherichia coli. J. Biol. Chem. 272 (1997) 9671–9676. [DOI] [PMID: 9092496]
3.  Rüdiger, W., Benz, J. and Guthoff, C. Detection and partial characterization of activity of chlorophyll synthetase in etioplast membranes. Eur. J. Biochem. 109 (1980) 193–200. [DOI] [PMID: 7408876]
[EC 2.5.1.62 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, PDB
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 2.5.1.68     
Accepted name: (2Z,6E)-farnesyl diphosphate synthase
Reaction: geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2Z,6E)-farnesyl diphosphate
For diagram of trans-polycis-polyprenol diphosphate biosynthesis, click here
Other name(s): (Z)-farnesyl diphosphate synthase; Z-farnesyl diphosphate synthase
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate geranylcistransferase
Comments: Requires Mg2+ or Mn2+ for activity. The product of this reaction is an intermediate in the synthesis of decaprenyl phosphate, which plays a central role in the biosynthesis of most features of the mycobacterial cell wall, including peptidoglycan, linker unit galactan and arabinan. Neryl diphosphate can also act as substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Schulbach, M.C., Mahapatra, S., Macchia, M., Barontini, S., Papi, C., Minutolo, F., Bertini, S., Brennan, P.J. and Crick, D.C. Purification, enzymatic characterization, and inhibition of the Z-farnesyl diphosphate synthase from Mycobacterium tuberculosis. J. Biol. Chem. 276 (2001) 11624–11630. [DOI] [PMID: 11152452]
[EC 2.5.1.68 created 2007, modified 2010]
 
 
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, PDB
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 2.5.1.71     
Accepted name: leachianone-G 2′′-dimethylallyltransferase
Reaction: prenyl diphosphate + leachianone G = diphosphate + sophoraflavanone G
For diagram of sophoraflavanone G biosynthesis, click here
Glossary: dimethylallyl = prenyl = 3-methylbut-2-en-1-yl
isopentenyl = 3-methylbut-3-en-1-yl
lavandulyl = 5-methyl-2-(prop-1-en-2-yl)hex-4-en-1-yl
leachianone G = (–)-(2S)-2′-hydroxy-8-prenylnaringenin = (–)-(2S)-2-(2,4-dihydroxyphenyl)-5,7-dihydroxy-8-(3-methylbut-2-en-1-yl)-2,3-dihydro-4H-chromen-4-one
sophoraflavanone G = (2S)-2-(2,4-dihydroxyphenyl)-5,7-dihydroxy-8-[(2R)-5-methyl-2-(prop-1-en-2-yl)hex-4-en-1-yl]-2,3-dihydro-4H-chromen-4-one
Other name(s): LG 2′′-dimethylallyltransferase; leachianone G 2′′-dimethylallyltransferase; LGDT; dimethylallyl-diphosphate:leachianone-G 2′′-dimethylallyltransferase
Systematic name: prenyl-diphosphate:leachianone-G 2′′-prenyltransferase
Comments: This membrane-bound enzyme is located in the plastids and requires Mg2+ for activity. The reaction forms the lavandulyl sidechain of sophoraflavanone G by transferring a prenyl group to the 2′′ position of another prenyl group attached at position 8 of leachianone G. The enzyme is specific for prenyl diphosphate as the prenyl donor, as it cannot be replaced by isopentenyl diphosphate or geranyl diphosphate. Euchrenone a7 (a 5-deoxy derivative of leachianone G) and kenusanone I (a 7-methoxy derivative of leachianone G) can also act as substrates, but more slowly. Along with EC 1.14.14.142 (8-dimethylallylnaringenin 2′-hydroxylase) and EC 2.5.1.70 (naringenin 8-dimethylallyltransferase), this enzyme forms part of the sophoraflavanone-G-biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhao, P., Inoue, K., Kouno, I. and Yamamoto, H. Characterization of leachianone G 2′′-dimethylallyltransferase, a novel prenyl side-chain elongation enzyme for the formation of the lavandulyl group of sophoraflavanone G in Sophora flavescens Ait. cell suspension cultures. Plant Physiol. 133 (2003) 1306–1313. [DOI] [PMID: 14551337]
[EC 2.5.1.71 created 2007]
 
 
EC 2.5.1.81     
Accepted name: geranylfarnesyl diphosphate synthase
Reaction: geranylgeranyl diphosphate + isopentenyl diphosphate = (2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): FGPP synthase; (all-E) geranylfarnesyl diphosphate synthase; GFPS; Fgs
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 1 isopentenyl unit)
Comments: The enzyme from Methanosarcina mazei is involved in biosynthesis of the polyprenyl side-chain of methanophenazine, an electron carrier utilized for methanogenesis. It prefers geranylgeranyl diphosphate and farnesyl diphosphate as allylic substrate [1]. The enzyme from Aeropyrum pernix prefers farnesyl diphosphate as allylic substrate. The enzyme is involved in the biosynthesis of C25-C25 membrane lipids [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ogawa, T., Yoshimura, T. and Hemmi, H. Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: Different role, different evolution. Biochem. Biophys. Res. Commun. 393 (2010) 16–20. [DOI] [PMID: 20097171]
2.  Tachibana, A., Yano, Y., Otani, S., Nomura, N., Sako, Y. and Taniguchi, M. Novel prenyltransferase gene encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, Aeropyrum pernix. Molecular evolution with alteration in product specificity. Eur. J. Biochem. 267 (2000) 321–328. [DOI] [PMID: 10632701]
3.  Tachibana, A. A novel prenyltransferase, farnesylgeranyl diphosphate synthase, from the haloalkaliphilic archaeon, Natronobacterium pharaonis. FEBS Lett. 341 (1994) 291–294. [DOI] [PMID: 8137956]
4.  Lee, P.C., Mijts, B.N., Petri, R., Watts, K.T. and Schmidt-Dannert, C. Alteration of product specificity of Aeropyrum pernix farnesylgeranyl diphosphate synthase (Fgs) by directed evolution. Protein Eng. Des. Sel. 17 (2004) 771–777. [DOI] [PMID: 15548566]
[EC 2.5.1.81 created 2010]
 
 
EC 2.5.1.82     
Accepted name: hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 2 (3-methylbut-3-en-1-yl diphosphate) = 2 diphosphate + all-trans-hexaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): HexPS(ambiguous); (all-E) hexaprenyl diphosphate synthase; (all-trans) hexaprenyl diphosphate synthase; hexaprenyl pyrophosphate synthase (ambiguous); HexPPs (ambiguous); hexaprenyl diphosphate synthase (ambiguous); geranylgeranyl-diphosphate:isopentenyl-diphosphate transferase (adding 2 isopentenyl units)
Systematic name: geranylgeranyl-diphosphate:3-methylbut-3-en-1-yl-diphosphate transferase (adding 2 units of 3-methylbut-3-en-1-yl)
Comments: The enzyme prefers geranylgeranyl diphosphate to farnesyl diphosphate as an allylic substrate and does not show activity for geranyl diphosphate and prenyl diphosphate. Requires Mg2+ [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Hemmi, H., Ikejiri, S., Yamashita, S. and Nishino, T. Novel medium-chain prenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus solfataricus. J. Bacteriol. 184 (2002) 615–620. [DOI] [PMID: 11790729]
2.  Hemmi, H., Noike, M., Nakayama, T. and Nishino, T. Change of product specificity of hexaprenyl diphosphate synthase from Sulfolobus solfataricus by introducing mimetic mutations. Biochem. Biophys. Res. Commun. 297 (2002) 1096–1101. [DOI] [PMID: 12372398]
3.  Sun, H.Y., Ko, T.P., Kuo, C.J., Guo, R.T., Chou, C.C., Liang, P.H. and Wang, A.H. Homodimeric hexaprenyl pyrophosphate synthase from the thermoacidophilic crenarchaeon Sulfolobus solfataricus displays asymmetric subunit structures. J. Bacteriol. 187 (2005) 8137–8148. [DOI] [PMID: 16291686]
[EC 2.5.1.82 created 1984 as EC 2.5.1.33, part transferred 2010 to EC 2.5.1.82]
 
 
EC 2.5.1.83     
Accepted name: hexaprenyl diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + 3 (3-methylbut-3-en-1-yl diphosphate) = 3 diphosphate + all-trans-hexaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): HexPS (ambiguous); hexaprenyl pyrophosphate synthetase (ambiguous); hexaprenyl diphosphate synthase (ambiguous); (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 3 isopentenyl units)
Systematic name: (2E,6E)-farnesyl-diphosphate:3-methylbut-3-en-1-yl-diphosphate farnesyltranstransferase (adding 3 units of 3-methylbut-3-en-1-yl)
Comments: The enzyme prefers farnesyl diphosphate to geranylgeranyl diphosphate as an allylic substrate and does not show activity for geranyl diphosphate and prenyl diphosphate [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Fujii, H., Koyama, T. and Ogura, K. Hexaprenyl pyrophosphate synthetase from Micrococcus luteus B-P 26. Separation of two essential components. J. Biol. Chem. 257 (1982) 14610–14612. [PMID: 7174655]
2.  Shimizu, N., Koyama, T. and Ogura, K. Molecular cloning, expression, and characterization of the genes encoding the two essential protein components of Micrococcus luteus B-P 26 hexaprenyl diphosphate synthase. J. Bacteriol. 180 (1998) 1578–1581. [PMID: 9515931]
3.  Nagaki, M., Kimura, K., Kimura, H., Maki, Y., Goto, E., Nishino, T. and Koyama, T. Artificial substrates of medium-chain elongating enzymes, hexaprenyl- and heptaprenyl diphosphate synthases. Bioorg. Med. Chem. Lett. 11 (2001) 2157–2159. [DOI] [PMID: 11514159]
[EC 2.5.1.83 created 1984 as EC 2.5.1.33, part transferred 2010 to EC 2.5.1.83]
 
 
EC 2.5.1.84     
Accepted name: all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific]
Reaction: geranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-nonaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Glossary: solanesyl diphosphate = all-trans-nonaprenyl diphosphate
Other name(s): nonaprenyl diphosphate synthase (ambiguous); solanesyl diphosphate synthase (ambiguous); SolPP synthase (ambiguous); SPP-synthase (ambiguous); SPP synthase (ambiguous); solanesyl-diphosphate synthase (ambiguous); OsSPS2
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 7 isopentenyl units)
Comments: (2E,6E)-Farnesyl diphosphate and geranylgeranyl diphosphate are less effective as substrates than geranyl diphosphate. The enzyme is involved in the synthesis of the side chain of menaquinone-9 [1]. In Oryza sativa the enzyme SPS2 is involved in providing solanesyl diphosphate for plastoquinone-9 formation [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sagami, H., Ogura, K. and Seto, S. Solanesyl pyrophosphate synthetase from Micrococcus lysodeikticus. Biochemistry 16 (1977) 4616–4622. [PMID: 911777]
2.  Fujii, H., Sagami, H., Koyama, T., Ogura, K., Seto, S., Baba, T. and Allen, C.M. Variable product specificity of solanesyl pyrophosphate synthetase. Biochem. Biophys. Res. Commun. 96 (1980) 1648–1653. [DOI] [PMID: 7447947]
3.  Ohara, K., Sasaki, K. and Yazaki, K. Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa. J. Exp. Bot. 61 (2010) 2683–2692. [DOI] [PMID: 20421194]
4.  Ohnuma, S., Koyama, T. and Ogura, K. Purification of solanesyl-diphosphate synthase from Micrococcus luteus. A new class of prenyltransferase. J. Biol. Chem. 266 (1991) 23706–23713. [PMID: 1748647]
5.  Gotoh, T., Koyama, T. and Ogura, K. Farnesyl diphosphate synthase and solanesyl diphosphate synthase reactions of diphosphate-modified allylic analogs: the significance of the diphosphate linkage involved in the allylic substrates for prenyltransferase. J. Biochem. 112 (1992) 20–27. [PMID: 1429508]
6.  Teclebrhan, H., Olsson, J., Swiezewska, E. and Dallner, G. Biosynthesis of the side chain of ubiquinone:trans-prenyltransferase in rat liver microsomes. J. Biol. Chem. 268 (1993) 23081–23086. [PMID: 8226825]
[EC 2.5.1.84 created 1972 as EC 2.5.1.11, part transferred 2010 to EC 2.5.1.84]
 
 
EC 2.5.1.85     
Accepted name: all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-nonaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Glossary: solanesyl diphosphate = all-trans-nonaprenyl diphosphate
Other name(s): nonaprenyl diphosphate synthase (ambiguous); solanesyl diphosphate synthase (ambiguous); At-SPS2; At-SPS1; SPS1; SPS2
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 5 isopentenyl units)
Comments: Geranylgeranyl diphosphate is preferred over farnesyl diphosphate as allylic substrate [1]. The plant Arabidopsis thaliana has two different enzymes that catalyse this reaction. SPS1 contributes to the biosynthesis of the ubiquinone side-chain while SPS2 supplies the precursor of the plastoquinone side-chains [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Hirooka, K., Bamba, T., Fukusaki, E. and Kobayashi, A. Cloning and kinetic characterization of Arabidopsis thaliana solanesyl diphosphate synthase. Biochem. J. 370 (2003) 679–686. [DOI] [PMID: 12437513]
2.  Hirooka, K., Izumi, Y., An, C.I., Nakazawa, Y., Fukusaki, E. and Kobayashi, A. Functional analysis of two solanesyl diphosphate synthases from Arabidopsis thaliana. Biosci. Biotechnol. Biochem. 69 (2005) 592–601. [DOI] [PMID: 15784989]
3.  Jun, L., Saiki, R., Tatsumi, K., Nakagawa, T. and Kawamukai, M. Identification and subcellular localization of two solanesyl diphosphate synthases from Arabidopsis thaliana. Plant Cell Physiol. 45 (2004) 1882–1888. [DOI] [PMID: 15653808]
[EC 2.5.1.85 created 1972 as EC 2.5.1.11, part transferred 2010 to EC 2.5.1.85]
 
 
EC 2.5.1.89     
Accepted name: tritrans,polycis-undecaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + tritrans,heptacis-undecaprenyl diphosphate
For diagram of di- and tritrans,polycis-polyprenol biosynthesis, click here
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 7 isopentenyl units)
Comments: This enzyme is involved in the biosynthesis of the glycosyl carrier lipid in some archaebacteria. Unlike EC 2.5.1.31, its counterpart in most bacteria, it prefers geranylgeranyl diphosphate to farnesyl diphosphate as the allylic substrate, resulting in production of a tritrans,polycis variant of undecaprenyl diphosphate [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hemmi, H., Yamashita, S., Shimoyama, T., Nakayama, T. and Nishino, T. Cloning, expression, and characterization of cis-polyprenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus acidocaldarius. J. Bacteriol. 183 (2001) 401–404. [DOI] [PMID: 11114943]
[EC 2.5.1.89 created 2010, modified 2011]
 
 
EC 2.5.1.93     
Accepted name: 4-hydroxybenzoate geranyltransferase
Reaction: geranyl diphosphate + 4-hydroxybenzoate = 3-geranyl-4-hydroxybenzoate + diphosphate
Other name(s): PGT1; PGT2; 4HB geranyltransferase; 4HB:geranyltransferase; p-hydroxybenzoate geranyltransferase; PHB geranyltransferase; geranyl diphosphate:4-hydroxybenzoate geranyltransferase
Systematic name: geranyl-diphosphate:4-hydroxybenzoate 3-geranyltransferase
Comments: The enzyme is involved in shikonin biosynthesis. It has a strict substrate specificity for geranyl diphosphate and an absolute requirement for Mg2+ [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ohara, K., Muroya, A., Fukushima, N. and Yazaki, K. Functional characterization of LePGT1, a membrane-bound prenyltransferase involved in the geranylation of p-hydroxybenzoic acid. Biochem. J. 421 (2009) 231–241. [DOI] [PMID: 19392660]
2.  Muhlenweg, A., Melzer, M., Li, S.M. and Heide, L. 4-Hydroxybenzoate 3-geranyltransferase from Lithospermum erythrorhizon: purification of a plant membrane-bound prenyltransferase. Planta 205 (1998) 407–413. [DOI] [PMID: 9640665]
3.  Yazaki, K., Kunihisa, M., Fujisaki, T. and Sato, F. Geranyl diphosphate:4-hydroxybenzoate geranyltransferase from Lithospermum erythrorhizon. Cloning and characterization of a key enzyme in shikonin biosynthesis. J. Biol. Chem. 277 (2002) 6240–6246. [DOI] [PMID: 11744717]
[EC 2.5.1.93 created 2010]
 
 
EC 2.5.1.99      
Deleted entry:  all-trans-phytoene synthase. The activity was an artifact caused by photoisomerization of the product of EC 2.5.1.32, 15-cis-phytoene synthase.
[EC 2.5.1.99 created 2012, deleted 2018]
 
 
EC 2.5.1.102     
Accepted name: geranyl-pyrophosphate—olivetolic acid geranyltransferase
Reaction: geranyl diphosphate + 2,4-dihydroxy-6-pentylbenzoate = diphosphate + cannabigerolate
For diagram of cannabinoid biosynthesis, click here
Glossary: 2,4-dihydroxy-6-pentylbenzoate = olivetolate
cannabigerolate = CBGA = 3-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-pentylbenzoate
cannabinerolate = 3-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-pentylbenzoate
Other name(s): GOT (ambiguous)
Systematic name: geranyl-diphosphate:olivetolate geranyltransferase
Comments: Part of the cannabinoids biosynthetic pathway of the plant Cannabis sativa. The enzyme can also use neryl diphosphate as substrate, forming cannabinerolate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fellermeier, M. and Zenk, M.H. Prenylation of olivetolate by a hemp transferase yields cannabigerolic acid, the precursor of tetrahydrocannabinol. FEBS Lett. 427 (1998) 283–285. [DOI] [PMID: 9607329]
[EC 2.5.1.102 created 2012]
 
 
EC 2.5.1.115     
Accepted name: homogentisate phytyltransferase
Reaction: phytyl diphosphate + homogentisate = diphosphate + 2-methyl-6-phytylbenzene-1,4-diol + CO2
For diagram of the homogentisate pathways, click here
Glossary: 2-methyl-6-phytylbenzene-1,4-diol = MPBQ
Other name(s): HPT; VTE2 (gene name)
Systematic name: phytyl-diphosphate:homogentisate phytyltransferase
Comments: Requires Mg2+ for activity [3]. Involved in the biosynthesis of the vitamin E tocopherols. While the enzyme from the cyanobacterium Synechocystis PCC 6803 has an appreciable activity with geranylgeranyl diphosphate (EC 2.5.1.116, homogentisate geranylgeranyltransferase), the enzyme from the plant Arabidopsis thaliana has only a low activity with that substrate [1,3,4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Collakova, E. and DellaPenna, D. Isolation and functional analysis of homogentisate phytyltransferase from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 127 (2001) 1113–1124. [PMID: 11706191]
2.  Savidge, B., Weiss, J.D., Wong, Y.H., Lassner, M.W., Mitsky, T.A., Shewmaker, C.K., Post-Beittenmiller, D. and Valentin, H.E. Isolation and characterization of homogentisate phytyltransferase genes from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 129 (2002) 321–332. [DOI] [PMID: 12011362]
3.  Sadre, R., Gruber, J. and Frentzen, M. Characterization of homogentisate prenyltransferases involved in plastoquinone-9 and tocochromanol biosynthesis. FEBS Lett. 580 (2006) 5357–5362. [DOI] [PMID: 16989822]
4.  Yang, W., Cahoon, R.E., Hunter, S.C., Zhang, C., Han, J., Borgschulte, T. and Cahoon, E.B. Vitamin E biosynthesis: functional characterization of the monocot homogentisate geranylgeranyl transferase. Plant J. 65 (2011) 206–217. [DOI] [PMID: 21223386]
[EC 2.5.1.115 created 2014]
 
 
EC 2.5.1.116     
Accepted name: homogentisate geranylgeranyltransferase
Reaction: geranylgeranyl diphosphate + homogentisate = diphosphate + 6-geranylgeranyl-2-methylbenzene-1,4-diol + CO2
For diagram of the homogentisate pathways, click here
Glossary: 6-geranylgeranyl-2-methylbenzene-1,4-diol = MGGBQ
Other name(s): HGGT; slr1736 (gene name)
Systematic name: geranylgeranyl-diphosphate:homogentisate geranylgeranyltransferase
Comments: Requires Mg2+ for activity. Involved in the biosynthesis of the vitamin E, tocotrienols. While the enzyme from the bacterium Synechocystis PCC 6803 has higher activity with phytyl diphosphate (EC 2.5.1.115, homogentisate phytyltransferase), the enzymes from barley, rice and wheat have only a low activity with that substrate [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Collakova, E. and DellaPenna, D. Isolation and functional analysis of homogentisate phytyltransferase from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 127 (2001) 1113–1124. [PMID: 11706191]
2.  Cahoon, E.B., Hall, S.E., Ripp, K.G., Ganzke, T.S., Hitz, W.D. and Coughlan, S.J. Metabolic redesign of vitamin E biosynthesis in plants for tocotrienol production and increased antioxidant content. Nat. Biotechnol. 21 (2003) 1082–1087. [DOI] [PMID: 12897790]
3.  Yang, W., Cahoon, R.E., Hunter, S.C., Zhang, C., Han, J., Borgschulte, T. and Cahoon, E.B. Vitamin E biosynthesis: functional characterization of the monocot homogentisate geranylgeranyl transferase. Plant J. 65 (2011) 206–217. [DOI] [PMID: 21223386]
[EC 2.5.1.116 created 2014]
 
 
EC 2.5.1.123     
Accepted name: flaviolin linalyltransferase
Reaction: geranyl diphosphate + flaviolin = 3-linalylflaviolin + diphosphate
For diagram of flaviolin metabolism, click here
Glossary: flaviolin = 2,5,7-trihydroxynaphthalene-1,4-dione
3-linalylflaviolin = 2,5,7-trihydroxy-3-(3,7-dimethylocta-1,6-dien-3-yl)naphthalene-1,4-dione
Other name(s): Fnq26
Systematic name: geranyl-diphosphate:flaviolin 3-linalyltransferase
Comments: Does not require Mg2+ or any other metal ions. Isolated from the bacterium Streptomyces cinnamonensis. In vitro the enzyme also forms traces of 3-geranylflaviolin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Haagen, Y., Unsold, I., Westrich, L., Gust, B., Richard, S.B., Noel, J.P. and Heide, L. A soluble, magnesium-independent prenyltransferase catalyzes reverse and regular C-prenylations and O-prenylations of aromatic substrates. FEBS Lett. 581 (2007) 2889–2893. [DOI] [PMID: 17543953]
[EC 2.5.1.123 created 2014]
 
 
EC 2.5.1.124     
Accepted name: 6-linalyl-2-O,3-dimethylflaviolin synthase
Reaction: geranyl diphosphate + 2-O,3-dimethylflaviolin = diphosphate + 6-linalyl-2-O,3-dimethylflaviolin
Glossary: flaviolin = 2,5,7-trihydroxy-1,4-naphthoquinone
2-O,3-dimethylflaviolin = 5,7-dihydroxy-2-methoxy-3-methylnaphthalene-1,4-dione
6-linalyl-2-O,3-dimethylflaviolin = 6-(3,7-dimethylocta-1,6-dien-3-yl)-5,7-dihydroxy-2-methoxy-3-methylnaphthalene-1,4-dione
Other name(s): Fur7; 6-(3,7-dimethylocta-1,6-dien-3-yl)-5,7-dihydroxy-2-methoxy-3-methylnaphthalene-1,4-dione synthase
Systematic name: geranyl-diphosphate:2-O-methyl-3-methylflaviolin geranyltransferase (6-linalyl-2-O,3-dimethylflaviolin-forming)
Comments: The enzyme is involved in biosynthesis of the polyketide-isoprenoid furaquinocin D in the bacterium Streptomyces sp. KO-3988. It catalyses the transfer of a geranyl group to 2-O,3-dimethylflaviolin to yield 6-linalyl-2-O,3-dimethylflaviolin and 7-O-geranyl-2-O,3-dimethylflaviolin (cf. EC 2.5.1.125, 7-geranyloxy-5-hydroxy-2-methoxy-3-methylnaphthalene-1,4-dione synthase) in a 10:1 ratio.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kumano, T., Tomita, T., Nishiyama, M. and Kuzuyama, T. Functional characterization of the promiscuous prenyltransferase responsible for furaquinocin biosynthesis: identification of a physiological polyketide substrate and its prenylated reaction products. J. Biol. Chem. 285 (2010) 39663–39671. [DOI] [PMID: 20937800]
[EC 2.5.1.124 created 2014]
 
 
EC 2.5.1.125     
Accepted name: 7-geranyloxy-5-hydroxy-2-methoxy-3-methylnaphthalene-1,4-dione synthase
Reaction: geranyl diphosphate + 2-O,3-dimethylflaviolin = diphosphate + 7-O-geranyl-2-O,3-dimethylflaviolin
Glossary: flaviolin = 2,5,7-trihydroxy-1,4-naphthoquinone
2-O,3-dimethylflaviolin = 5,7-dihydroxy-2-methoxy-3-methylnaphthalene-1,4-dione
7-O-geranyl-2-O,3-dimethylflaviolin = 7-{[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-5-hydroxy-2-methoxy-3-methylnaphthalene-1,4-dione
Other name(s): Fur7
Systematic name: geranyl-diphosphate:2-O,3-dimethylflaviolin geranyltransferase (7-O-geranyl-2-O,3-dimethylflaviolin-forming)
Comments: The enzyme is involved in furaquinocin biosynthesis in the bacterium Streptomyces sp. KO-3988. It catalyses the transfer of a geranyl group to 2-O,3-dimethylflaviolin to yield 7-O-geranyl-2-O,3-dimethylflaviolin and 6-linalyl-2-O,3-dimethylflaviolin (cf. EC 2.5.1.124, 6-linalyl-2-O,3-dimethylflaviolin synthase) in a 1:10 ratio.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kumano, T., Tomita, T., Nishiyama, M. and Kuzuyama, T. Functional characterization of the promiscuous prenyltransferase responsible for furaquinocin biosynthesis: identification of a physiological polyketide substrate and its prenylated reaction products. J. Biol. Chem. 285 (2010) 39663–39671. [DOI] [PMID: 20937800]
[EC 2.5.1.125 created 2014]
 
 
EC 2.5.1.130     
Accepted name: 2-carboxy-1,4-naphthoquinone phytyltransferase
Reaction: phytyl diphosphate + 2-carboxy-1,4-naphthoquinone = demethylphylloquinone + diphosphate + CO2
For diagram of vitamin K biosynthesis, click here
Glossary: 2-carboxy-1,4-naphthoquinone = 1,4-dioxo-2-naphthoic acid
Other name(s): menA (gene name); ABC4 (gene name); 1,4-dioxo-2-naphthoate phytyltransferase; 1,4-diketo-2-naphthoate phytyltransferase
Systematic name: phytyl-diphosphate:2-carboxy-1,4-naphthoquinone phytyltransferase
Comments: This enzyme, found in plants and cyanobacteria, catalyses a step in the synthesis of phylloquinone (vitamin K1), an electron carrier associated with photosystem I. The enzyme catalyses the transfer of the phytyl chain synthesized by EC 1.3.1.83, geranylgeranyl diphosphate reductase, to 2-carboxy-1,4-naphthoquinone.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Johnson, T.W., Shen, G., Zybailov, B., Kolling, D., Reategui, R., Beauparlant, S., Vassiliev, I.R., Bryant, D.A., Jones, A.D., Golbeck, J.H. and Chitnis, P.R. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. PCC 6803. J. Biol. Chem. 275 (2000) 8523–8530. [DOI] [PMID: 10722690]
2.  Shimada, H., Ohno, R., Shibata, M., Ikegami, I., Onai, K., Ohto, M.A. and Takamiya, K. Inactivation and deficiency of core proteins of photosystems I and II caused by genetical phylloquinone and plastoquinone deficiency but retained lamellar structure in a T-DNA mutant of Arabidopsis. Plant J. 41 (2005) 627–637. [DOI] [PMID: 15686525]
[EC 2.5.1.130 created 2015]
 
 
EC 2.5.1.133     
Accepted name: bacteriochlorophyll a synthase
Reaction: geranylgeranyl diphosphate + bacteriochlorophyllide a = geranylgeranyl-bacteriochlorophyllide a + diphosphate
For diagram of bacteriochlorophyl a biosynthesis, click here
Other name(s): bchG (gene name)
Systematic name: geranylgeranyl-diphosphate:bacteriochlorophyllide-a geranylgeranytransferase
Comments: The enzyme catalyses the addition of a geranylgeranyl hydrophobic chain to bacteriochlorophyllide a via an ester bond with the 17-propionate residue. The side chain is later modified to a phytyl chain, resulting in bacteriochlorophyll a.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Oster, U., Bauer, C.E. and Rüdiger, W. Characterization of chlorophyll a and bacteriochlorophyll a synthases by heterologous expression in Escherichia coli. J. Biol. Chem. 272 (1997) 9671–9676. [DOI] [PMID: 9092496]
2.  Addlesee, H.A., Fiedor, L. and Hunter, C.N. Physical mapping of bchG, orf427, and orf177 in the photosynthesis gene cluster of Rhodobacter sphaeroides: functional assignment of the bacteriochlorophyll synthetase gene. J. Bacteriol. 182 (2000) 3175–3182. [DOI] [PMID: 10809697]
3.  Garcia-Gil, L.J., Gich, F.B. and Fuentes-Garcia, X. A comparative study of bchG from green photosynthetic bacteria. Arch. Microbiol. 179 (2003) 108–115. [DOI] [PMID: 12560989]
4.  Saga, Y., Hirota, K., Harada, J. and Tamiaki, H. In vitro enzymatic activities of bacteriochlorophyll a synthase derived from the green sulfur photosynthetic bacterium Chlorobaculum tepidum. Biochemistry 54 (2015) 4998–5005. [DOI] [PMID: 26258685]
[EC 2.5.1.133 created 2016]
 
 
EC 2.5.1.138     
Accepted name: coumarin 8-geranyltransferase
Reaction: (1) geranyl diphosphate + umbelliferone = diphosphate + 8-geranylumbelliferone
(2) geranyl diphosphate + esculetin = diphosphate + 8-geranylesculetin
Glossary: geranyl diphosphate = (2E)-3,7-dimethylocta-2,6-dien-1-yl diphosphate
esculetin = 6,7-dihydroxy-1-benzopyran-2-one = 6,7-dihydroxycoumarin
umbelliferone = 7-hydroxy-1-benzopyran-2-one = 7-hydroxycoumarin
Other name(s): ClPT1
Systematic name: geranyl-diphosphate:umbelliferone 8-geranyltransferase
Comments: The enzyme, characterized from the plant Citrus limon, is specific for geranyl diphosphate as a prenyl donor. It also has low activity with the coumarins 5,7-dihydroxycoumarin and 5-methoxy-7-hydroxycoumarin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Munakata, R., Inoue, T., Koeduka, T., Karamat, F., Olry, A., Sugiyama, A., Takanashi, K., Dugrand, A., Froelicher, Y., Tanaka, R., Uto, Y., Hori, H., Azuma, J., Hehn, A., Bourgaud, F. and Yazaki, K. Molecular cloning and characterization of a geranyl diphosphate-specific aromatic prenyltransferase from lemon. Plant Physiol. 166 (2014) 80–90. [DOI] [PMID: 25077796]
[EC 2.5.1.138 created 2017]
 
 
EC 2.5.1.146     
Accepted name: 3-geranyl-3-[(Z)-2-isocyanoethenyl]indole synthase
Reaction: geranyl diphosphate + 3-[(Z)-2-isocyanoethenyl]-1H-indole = 3-geranyl-3-[(Z)-2-isocyanoethenyl]-1H-indole + diphosphate
Other name(s): famD2 (gene name)
Systematic name: geranyl-diphosphate:3-[(Z)-2-isocyanoethenyl]-1H-indole geranyltransferase
Comments: The enzyme, characterized from the cyanobacterium Fischerella ambigua UTEX 1903, participates in the biosynthesis of hapalindole-type alkaloids.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Li, S., Lowell, A.N., Yu, F., Raveh, A., Newmister, S.A., Bair, N., Schaub, J.M., Williams, R.M. and Sherman, D.H. Hapalindole/ambiguine biogenesis Is mediated by a Cope rearrangement, C-C bond-forming cascade. J. Am. Chem. Soc. 137 (2015) 15366–15369. [DOI] [PMID: 26629885]
[EC 2.5.1.146 created 2018]
 
 
EC 2.5.1.148     
Accepted name: lycopaoctaene synthase
Reaction: 2 geranylgeranyl diphosphate + NADPH + H+ = lycopaoctaene + 2 diphosphate + NADP+ (overall reaction)
(1a) 2 geranylgeranyl diphosphate = diphosphate + prephytoene diphosphate
(1b) prephytoene diphosphate + NADPH + H+ = lycopaoctaene + diphosphate + NADP+
For diagram of squalene, phytoene and 4,4′-diapophytoene biosynthesis, click here
Glossary: lycopaoctaene = 15,15′-dihydrophytoene = (6E,10E,14E,18E,22E,26E)-2,6,10,14,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaene
Other name(s): LOS (gene name)
Systematic name: geranylgeranyl-diphosphate:geranylgeranyl diphosphate geranylgeranyltransferase
Comments: The enzyme, characterized from the green microalga Botryococcus braunii race L, in involved in biosynthesis of (14E,18E)-lycopadiene. In vitro, the enzyme can accept (2E,6E)-farnesyl diphosphate and phytyl diphosphate as substrates, and is also able to catalyse the condensation of two different substrate molecules, forming chimeric products. However, the use of these alternative substrates is not significant in vivo.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Thapa, H.R., Naik, M.T., Okada, S., Takada, K., Molnar, I., Xu, Y. and Devarenne, T.P. A squalene synthase-like enzyme initiates production of tetraterpenoid hydrocarbons in Botryococcus braunii Race L. Nat. Commun. 7:11198 (2016). [PMID: 27050299]
2.  Thapa, H.R., Tang, S., Sacchettini, J.C. and Devarenne, T.P. Tetraterpene synthase substrate and product specificity in the green microalga Botryococcus braunii Race L. ACS Chem. Biol. 12 (2017) 2408–2416. [PMID: 28813599]
[EC 2.5.1.148 created 2018]
 
 
EC 2.5.1.155     
Accepted name: phosphoglycerol geranylfarnesyltransferase
Reaction: all-trans-pentaprenyl diphosphate + sn-glycerol 1-phosphate = sn-3-O-(farnesylgeranyl)glycerol 1-phosphate + diphosphate
Other name(s): GFGP synthase
Systematic name: all-trans pentaprenyl diphosphate:sn-glycerol-1-phosphate pentaprenyltransferase
Comments: The enzyme, characterized from the archaeon Aeropyrum pernix, catalyses the first pathway-specific step in the biosynthesis of the core membrane C25,C25-diether lipids in some archaea. It does not act on geranylgeranyl diphosphate. cf. EC 2.5.1.41, phosphoglycerol geranylgeranyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yoshida, R., Yoshimura, T. and Hemmi, H. Biosynthetic machinery for C25,C25-diether archaeal lipids from the hyperthermophilic archaeon Aeropyrum pernix. Biochem. Biophys. Res. Commun. 497 (2018) 87–92. [DOI] [PMID: 29427665]
[EC 2.5.1.155 created 2022]
 
 
EC 2.9.1.3     
Accepted name: tRNA 2-selenouridine synthase
Reaction: selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O = 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate (overall reaction)
(1a) geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA = 5-methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA + diphosphate
(1b) selenophosphate + 5-methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA = 5-methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol
(1c) 5-methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA + H2O = 5-methylaminomethyl-2-selenouridine34 in tRNA + phosphate
Other name(s): selU (gene name); mnmH (gene name); ybbB (gene name); sufY (gene name)
Systematic name: geranyl diphosphate/selenophosphate:tRNA 5-methylaminomethyl-2-thiouridine34 geranyl/selenophosphatetransferase
Comments: This bacterial enzyme converts 5-methylaminomethyl-2-uridine and 5-carboxymethylaminomethyl-2-uridine to the respective selenouridine forms in a two-step process that involves geranylation and subsequent phosphoselenation of the resulting geranylated intermediates. The resultant seleno-phosphorylated uridine intermediates further react with a water molecule to release a phosphate anion and 2-selenouridine tRNA. The enzyme contains a rhodanese domain.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bartos, P., Maciaszek, A., Rosinska, A., Sochacka, E. and Nawrot, B. Transformation of a wobble 2-thiouridine to 2-selenouridine via S-geranyl-2-thiouridine as a possible cellular pathway. Bioorg. Chem. 56 (2014) 49–53. [PMID: 24971911]
2.  Jager, G., Chen, P. and Bjork, G.R. Transfer RNA bound to mnmh protein is enriched with geranylated tRNA—a possible intermediate in its selenation. PLoS One 11:e0153488 (2016). [PMID: 27073879]
3.  Sierant, M., Leszczynska, G., Sadowska, K., Komar, P., Radzikowska-Cieciura, E., Sochacka, E. and Nawrot, B. Escherichia coli tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA via S-geranylated-intermediate. FEBS Lett. 592 (2018) 2248–2258. [PMID: 29862510]
[EC 2.9.1.3 created 2020]
 
 
EC 3.1.3.98      
Transferred entry: geranyl diphosphate phosphohydrolase, transferred to EC 3.6.1.68, geranyl diphosphate phosphohydrolase
[EC 3.1.3.98 created 2015, deleted 2016]
 
 
EC 3.1.7.4      
Deleted entry: Now recognized as two enzymes EC 4.2.1.133, copal-8-ol diphosphate synthase and EC 4.2.3.141 sclareol synthase
[EC 3.1.7.4 created 2008, deleted 2013]
 
 
EC 3.1.7.5     
Accepted name: geranylgeranyl diphosphate diphosphatase
Reaction: geranylgeranyl diphosphate + H2O = geranylgeraniol + diphosphate
For diagram of acyclic diterpenoid biosynthesis, click here
Glossary: plaunotol = 18-hydroxygeranylgeraniol
Other name(s): geranylgeranyl diphosphate phosphatase
Systematic name: geranyl-diphosphate diphosphohydrolase
Comments: Involved in the biosynthesis of plaunotol. There are two isoenzymes with different ion requirements. Neither require Mg2+ but in addition PII is inhibited by Zn2+, Mn2+ and Co2+. It is not known which isoenzyme is involved in plaunotol biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Nualkaew, N., De-Eknamkul, W., Kutchan, T.M. and Zenk, M.H. Membrane-bound geranylgeranyl diphosphate phosphatases: purification and characterization from Croton stellatopilosus leaves. Phytochemistry 67 (2006) 1613–1620. [DOI] [PMID: 16445953]
[EC 3.1.7.5 created 2009]
 
 
EC 3.1.7.10     
Accepted name: (13E)-labda-7,13-dien-15-ol synthase
Reaction: geranylgeranyl diphosphate + H2O = (13E)-labda-7,13-dien-15-ol + diphosphate
For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here and for diagram of sclareol and (13e)-labda-7,13-dien-15-ol biosynthesis, click here
Other name(s): labda-7,13E-dien-15-ol synthase
Systematic name: geranylgeranyl-diphosphate diphosphohydrolase [(13E)-labda-7,13-dien-15-ol-forming]
Comments: The enzyme from the lycophyte Selaginella moellendorffii is bifunctional, initially forming (13E)-labda-7,13-dien-15-yl diphosphate, which is hydrolysed to the alcohol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mafu, S., Hillwig, M.L. and Peters, R.J. A novel labda-7,13E-dien-15-ol-producing bifunctional diterpene synthase from Selaginella moellendorffii. ChemBioChem 12 (2011) 1984–1987. [DOI] [PMID: 21751328]
[EC 3.1.7.10 created 2012]
 
 
EC 3.1.7.11     
Accepted name: geranyl diphosphate diphosphatase
Reaction: geranyl diphosphate + H2O = geraniol + diphosphate
For diagram of acyclic monoterpenoid biosynthesis, click here
Other name(s): geraniol synthase; geranyl pyrophosphate pyrophosphatase; GES; CtGES
Systematic name: geranyl-diphosphate diphosphohydrolase
Comments: Isolated from Ocimum basilicum (basil) and Cinnamomum tenuipile (camphor tree). Requires Mg2+ or Mn2+. Geraniol is labelled when formed in the presence of [18O]H2O. Thus mechanism involves a geranyl cation [1]. Neryl diphosphate is hydrolysed more slowly. May be the same as EC 3.1.7.3 monoterpenyl-diphosphatase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Iijima, Y., Gang, D.R., Fridman, E., Lewinsohn, E. and Pichersky, E. Characterization of geraniol synthase from the peltate glands of sweet basil. Plant Physiol. 134 (2004) 370–379. [DOI] [PMID: 14657409]
2.  Yang, T., Li, J., Wang, H.X. and Zeng, Y. A geraniol-synthase gene from Cinnamomum tenuipilum. Phytochemistry 66 (2005) 285–293. [DOI] [PMID: 15680985]
[EC 3.1.7.11 created 2012]
 
 
EC 3.6.1.68     
Accepted name: geranyl diphosphate phosphohydrolase
Reaction: geranyl diphosphate + H2O = geranyl phosphate + phosphate
For diagram of acyclic monoterpenoid biosynthesis, click here
Other name(s): NUDX1 (gene name)
Systematic name: geranyl-diphosphate phosphohydrolase
Comments: The enzyme, characterized from roses, is involved in a cytosolic pathway for the biosynthesis of free monoterpene alcohols that contribute to fragrance. In vitro the enzyme also acts on (2E,6E)-farnesyl diphosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Magnard, J.L., Roccia, A., Caissard, J.C., Vergne, P., Sun, P., Hecquet, R., Dubois, A., Hibrand-Saint Oyant, L., Jullien, F., Nicole, F., Raymond, O., Huguet, S., Baltenweck, R., Meyer, S., Claudel, P., Jeauffre, J., Rohmer, M., Foucher, F., Hugueney, P., Bendahmane, M. and Baudino, S. Plant volatiles. Biosynthesis of monoterpene scent compounds in roses. Science 349 (2015) 81–83. [DOI] [PMID: 26138978]
[EC 3.6.1.68 created 2015 as EC 3.1.3.98, transferred 2016 to EC 3.6.1.68]
 
 
EC 4.2.1.133     
Accepted name: copal-8-ol diphosphate hydratase
Reaction: (13E)-8α-hydroxylabd-13-en-15-yl diphosphate = geranylgeranyl diphosphate + H2O
For diagram of hydroxylabdenyl diphosphate derived diterpenoids, click here
Glossary: (13E)-8α-hydroxylabd-13-en-15-yl diphosphate = 8-hydroxycopalyl diphosphate
Other name(s): CcCLS
Systematic name: geranylgeranyl-diphosphate hydro-lyase [(13E)-8α-hydroxylabd-13-en-15-yl diphosphate-forming]
Comments: Requires Mg2+. The enzyme was characterized from the plant Cistus creticus subsp. creticus.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Falara, V., Pichersky, E. and Kanellis, A.K. A copal-8-ol diphosphate synthase from the angiosperm Cistus creticus subsp. creticus is a putative key enzyme for the formation of pharmacologically active, oxygen-containing labdane-type diterpenes. Plant Physiol. 154 (2010) 301–310. [DOI] [PMID: 20595348]
[EC 4.2.1.133 created 2012]
 
 
EC 4.2.1.173     
Accepted name: ent-8α-hydroxylabd-13-en-15-yl diphosphate synthase
Reaction: ent-8α-hydroxylabd-13-en-15-yl diphosphate = geranylgeranyl diphosphate + H2O
For diagram of (#150)-kolavenyl diphosphate derived diterpenoids, click here
Other name(s): SmCPS4
Systematic name: geranylgeranyl-diphosphate hydro-lyase (ent-8α-hydroxylabd-13-en-15-yl diphosphate-forming)
Comments: Isolated from the plant Salvia miltiorrhiza (red sage).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cui, G., Duan, L., Jin, B., Qian, J., Xue, Z., Shen, G., Snyder, J.H., Song, J., Chen, S., Huang, L., Peters, R.J. and Qi, X. Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza. Plant Physiol. 169 (2015) 1607–1618. [DOI] [PMID: 26077765]
[EC 4.2.1.173 created 2017]
 
 
EC 4.2.1.174     
Accepted name: peregrinol diphosphate synthase
Reaction: peregrinol diphosphate = geranylgeranyl diphosphate + H2O
For diagram of hydroxylabdenyl diphosphate derived diterpenoids, click here
Glossary: peregrinol diphosphate = (13E)-9-hydroxy-8α-labda-13-en-15-yl diphosphate
Other name(s): MvCPS1
Systematic name: geranylgeranyl-diphosphate hydro-lyase (peregrinol-diphosphate-forming)
Comments: Isolated from the plant Marrubium vulgare (white horehound). Involved in marrubiin biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zerbe, P., Chiang, A., Dullat, H., O'Neil-Johnson, M., Starks, C., Hamberger, B. and Bohlmann, J. Diterpene synthases of the biosynthetic system of medicinally active diterpenoids in Marrubium vulgare. Plant J. 79 (2014) 914–927. [DOI] [PMID: 24990389]
[EC 4.2.1.174 created 2017]
 
 
EC 4.2.3.8     
Accepted name: casbene synthase
Reaction: geranylgeranyl diphosphate = casbene + diphosphate
For diagram of cembrene and related diterpenoids, click here
Other name(s): casbene synthetase; geranylgeranyl-diphosphate diphosphate-lyase (cyclizing)
Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (cyclizing, casbene-forming)
Comments: The enzyme from castor bean (Ricinus communis) produces the antifungal diterpene casbene.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 69106-45-2
References:
1.  Moesta, P. and West, C.A. Casbene synthetase: regulation of phytoalexin biosynthesis in Ricinus communis L. seedlings. Purification of casbene synthetase and regulation of its biosynthesis during elicitation. Arch. Biochem. Biophys. 238 (1985) 325–333. [DOI] [PMID: 3985625]
2.  Mau, C.J. and West, C.A. Cloning of casbene synthase cDNA: evidence for conserved structural features among terpenoid cyclases in plants. Proc. Natl. Acad. Sci. USA 91 (1994) 8497–8501. [DOI] [PMID: 8078910]
[EC 4.2.3.8 created 1989 as EC 4.6.1.7, transferred 2000 to EC 4.2.3.8, modified 2024]
 
 


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