The Enzyme Database

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EC 1.17.7.4     
Accepted name: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase
Reaction: (1) 3-methylbut-3-en-1-yl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O = (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
(2) prenyl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O = (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+
For diagram of Non-Mevalonate terpenoid biosynthesis, click here
Glossary: isopentenyl = 3-methylbut-3-en-1-yl
prenyl = 3-methylbut-2-en-1-yl
Other name(s): isopentenyl-diphosphate:NADP+ oxidoreductase; LytB; (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase; HMBPP reductase; IspH; LytB/IspH; isopentenyl-diphosphate:ferredoxin oxidoreductase
Systematic name: 3-methylbut-3-en-1-yl-diphosphate:ferredoxin oxidoreductase
Comments: An iron-sulfur protein that contains either a [3Fe-4S] [6] or a [4Fe-4S] [5] cluster. This enzyme forms a system with a ferredoxin or a flavodoxin and an NAD(P)H-dependent reductase. This is the last enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. This pathway, also known as the 1-deoxy-D-xylulose 5-phosphate (DOXP) or as the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway, is found in most bacteria and in plant chloroplasts. The enzyme acts in the reverse direction, producing a 5:1 mixture of 3-methylbut-3-en-1-yl diphosphate and prenyl diphosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 512789-14-9
References:
1.  Rohdich, F., Hecht, S., Gärtner, K., Adam, P., Krieger, C., Amslinger, S., Arigoni, D., Bacher, A. and Eisenreich, W. Studies on the nonmevalonate terpene biosynthetic pathway: Metabolic role of IspH (LytB) protein. Proc. Natl. Acad. Sci. USA 99 (2002) 1158–1163. [DOI] [PMID: 11818558]
2.  Hintz, M., Reichenberg, A., Altincicek, B., Bahr, U., Gschwind, R.M., Kollas, A.-K., Beck, E., Wiesner, J., Eberl, M. and Jomaa, H. Identification of (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate as a major activator for human T cells in Escherichia coli. FEBS Lett. 509 (2001) 317–322. [DOI] [PMID: 11741609]
3.  Charon, L., Pale-Grosdemange, C. and Rohmer, M. On the reduction steps in the mevalonate independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis in the bacterium Zymomonas mobilis. Tetrahedron Lett. 40 (1999) 7231–7234.
4.  Röhrich, R.C., Englert, N., Troschke, K., Reichenberg, A., Hintz, M., Seeber, F., Balconi, E., Aliverti, A., Zanetti, G., Köhler, U., Pfeiffer, M., Beck, E., Jomaa, H. and Wiesner, J. Reconstitution of an apicoplast-localised electron transfer pathway involved in the isoprenoid biosynthesis of Plasmodium falciparum. FEBS Lett. 579 (2005) 6433–6438. [DOI] [PMID: 16289098]
5.  Wolff, M., Seemann, M., Bui, T.S.B., Frapart, Y., Tritsch, D., Garcia Estrabot, A., Rodríguez-Concepción, M., Boronat, A., Marquet, A. and Rohmer, M. Isoprenoid biosynthesis via the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (LytB/IspH) from Escherichia coli is a [4Fe-4S] protein. FEBS Lett. 541 (2003) 115–120. [DOI] [PMID: 12706830]
6.  Gräwert, T., Kaiser, J., Zepeck, F., Laupitz, R., Hecht, S., Amslinger, S., Schramek, N., Schleicher, E., Weber, S., Haslbeck, M., Buchner, J., Rieder, C., Arigoni, D., Bacher, A., Eisenreich, W. and Rohdich, F. IspH protein of Escherichia coli: studies on iron-sulfur cluster implementation and catalysis. J. Am. Chem. Soc. 126 (2004) 12847–12855. [DOI] [PMID: 15469281]
[EC 1.17.7.4 created 2003 as EC 1.17.1.2, modified 2009, transferred 2016 to EC 1.17.7.4]
 
 
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 2.5.1.69     
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 2.5.1.71     
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 2.5.1.82     
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
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
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 2.5.1.142     
Accepted name: nerylneryl diphosphate synthase
Reaction: prenyl diphosphate + 3 (3-methylbut-3-en-1-yl diphosphate) = 3 diphosphate + nerylneryl diphosphate
(1a) prenyl diphosphate + 3-methylbut-3-en-1-yl diphosphate = diphosphate + neryl diphosphate
(1b) neryl diphosphate + 3-methylbut-3-en-1-yl diphosphate = diphosphate + (2Z,6Z)-farnesyl diphosphate
(1c) (2Z,6Z)-farnesyl diphosphate + 3-methylbut-3-en-1-yl diphosphate = diphosphate + nerylneryl diphosphate
For diagram of all-cis-polyprenyl diphosphate, click here
Glossary: nerylneryl diphosphate = all-cis-tetraprenyl diphosphate
Other name(s): CPT2; dimethylallyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 3 isopentenyl units)
Systematic name: prenyl-diphosphate:3-methylbut-3-en-1-yl-diphosphate cistransferase (adding 3 units of 3-methylbut-3-en-1-yl)
Comments: Isolated from the plant Solanum lycopersicum (tomato).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Akhtar, T.A., Matsuba, Y., Schauvinhold, I., Yu, G., Lees, H.A., Klein, S.E. and Pichersky, E. The tomato cis-prenyltransferase gene family. Plant J. 73 (2013) 640–652. [DOI] [PMID: 23134568]
2.  Matsuba, Y., Zi, J., Jones, A.D., Peters, R.J. and Pichersky, E. Biosynthesis of the diterpenoid lycosantalonol via nerylneryl diphosphate in Solanum lycopersicum. PLoS One 10:e0119302 (2015). [DOI] [PMID: 25786135]
[EC 2.5.1.142 created 2017]
 
 
EC 2.7.4.26     
Accepted name: isopentenyl phosphate kinase
Reaction: ATP + 3-methylbut-3-en-1-yl phosphate = ADP + 3-methylbut-3-en-1-yl diphosphate
For diagram of the archaeal mevalonate pathway, click here
Other name(s): ATP:isopentenyl phosphate phosphotransferase
Systematic name: ATP:3-methylbut-3-en-1-yl-phosphate phosphotransferase
Comments: The enzyme is involved in the mevalonate pathway in Archaea [1]. The activity has also been identified in the plant Mentha piperita (peppermint) [2]. It is strictly specific for ATP but can use other phosphate acceptors such as prenyl phosphate, geranyl phosphate, or fosfomycin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Grochowski, L.L., Xu, H. and White, R.H. Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate. J. Bacteriol. 188 (2006) 3192–3198. [DOI] [PMID: 16621811]
2.  Lange, B.M. and Croteau, R. Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway: isopentenyl monophosphate kinase catalyzes the terminal enzymatic step. Proc. Natl. Acad. Sci. USA 96 (1999) 13714–13719. [DOI] [PMID: 10570138]
3.  Chen, M. and Poulter, C.D. Characterization of thermophilic archaeal isopentenyl phosphate kinases. Biochemistry 49 (2010) 207–217. [DOI] [PMID: 19928876]
4.  Mabanglo, M.F., Schubert, H.L., Chen, M., Hill, C.P. and Poulter, C.D. X-ray structures of isopentenyl phosphate kinase. ACS Chem. Biol. 5 (2010) 517–527. [DOI] [PMID: 20402538]
[EC 2.7.4.26 created 2012]
 
 
EC 4.2.3.26     
Accepted name: R-linalool synthase
Reaction: geranyl diphosphate + H2O = (3R)-linalool + diphosphate
For diagram of acyclic monoterpenoid biosynthesis, click here
Glossary: (3R)-linalool = (3R)-3,7-dimethylocta-1,6-dien-3-ol
Other name(s): (3R)-linalool synthase; (–)-3R-linalool synthase
Systematic name: geranyl-diphosphate diphosphate-lyase [(3R)-linalool-forming]
Comments: Geranyl diphosphate cannot be replaced by isopentenyl diphosphate (3-methylbut-3-en-1-yl diphosphate), prenyl diphosphate, farnesyl diphosphate or geranylgeranyl diphosphate as substrate [1]. Requires Mg2+ or Mn2+ for activity. Unlike many other monoterpene synthases, only a single product, (3R)-linalool, is formed.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 254993-26-5
References:
1.  Jia, J.W., Crock, J., Lu, S., Croteau, R. and Chen, X.Y. (3R)-Linalool synthase from Artemisia annua L.: cDNA isolation, characterization, and wound induction. Arch. Biochem. Biophys. 372 (1999) 143–149. [DOI] [PMID: 10562427]
2.  Crowell, A.L., Williams, D.C., Davis, E.M., Wildung, M.R. and Croteau, R. Molecular cloning and characterization of a new linalool synthase. Arch. Biochem. Biophys. 405 (2002) 112–121. [DOI] [PMID: 12176064]
[EC 4.2.3.26 created 2006]
 
 
EC 5.3.3.2     
Accepted name: isopentenyl-diphosphate Δ-isomerase
Reaction: 3-methylbut-3-en-1-yl diphosphate = prenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): isopentenylpyrophosphate Δ-isomerase; methylbutenylpyrophosphate isomerase; isopentenylpyrophosphate isomerase; isopentenyl-diphosphate Δ32-isomerase
Systematic name: 3-methylbut-3-en-1-yl-diphosphate Δ32-isomerase
Comments: The enzyme from Streptomyces sp. strain CL190 requires FMN and NAD(P)H as cofactors. Activity is reduced if FMN is replaced by FAD, but the enzyme becomes inactive when NAD(P)H is replaced by NAD+ or NADP+. That enzyme also requires Mg2+, Mn2+ or Ca2+ for activity.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9033-27-6
References:
1.  Kaneda, K., Kuzuyama, T., Takagi, M., Hayakawa, Y. and Seto, H. An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190. Proc. Natl. Acad. Sci. USA 98 (2001) 932–937. [DOI] [PMID: 11158573]
2.  Bishop, J.M. Cellular oncogenes and retroviruses. Annu. Rev. Biochem. 52 (1983) 301–354. [DOI] [PMID: 6351725]
3.  Agranoff, B.W., Eggerer, H., Henning, U. and Lynen, F. Biosynthesis of terpenes. VII. Isopentenyl pyrophosphate isomerase. J. Biol. Chem. 235 (1960) 326–332. [PMID: 13792054]
[EC 5.3.3.2 created 1961, modified 2002]
 
 


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