Escherichia coli K-12 substr. MG1655 Pathway: trans, trans-farnesyl diphosphate biosynthesis
Traceable author statement to experimental support

Pathway diagram: trans, trans-farnesyl diphosphate biosynthesis

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Schematic showing all replicons, marked with selected genes

Synonyms: FPP biosynthesis, trans, trans-farnesyl diphosphate biosynthesis

Superclasses: BiosynthesisCofactors, Prosthetic Groups, Electron Carriers BiosynthesisPolyprenyl BiosynthesisAll-Trans-Farnesyl-PP-Biosynthesis

General Background

In E. coli the isoprenoid diphosphate (2E,6E)-farnesyl diphosphate (FPP) is a precursor of the three major isoprenoid quinones ubiquinone, demethylmenaquinone, and menaquinone. These quinones function as electron carriers within the cytoplasmic membrane. Each is required for respiration using different, but overlapping subsets of final electron acceptors (see pathways ubiquinol-8 biosynthesis (prokaryotic) demethylmenaquinol-8 biosynthesis I and menaquinol-8 biosynthesis). Their isoprenoid side chain is biosynthesized as shown in this pathway and pathway octaprenyl diphosphate biosynthesis. In addition, FPP is also a precursor of di-trans,octa-cis-undecaprenyl diphosphate, an isoprenoid diphosphate that participates in pathways enterobacterial common antigen biosynthesis and peptidoglycan biosynthesis I (meso-diaminopimelate containing).

About This Pathway

In the first reaction isopentenyl diphosphate isomerase catalyzes the reversible isomerization of isopentenyl diphosphate (IPP) to dimethylallyl diphosphate (DMAPP), a key step in the biosynthesis of isoprenoids. In E. coli these two compounds are bisoynthesized by the methylerythritol phosphate pathway I. In the second and third reactions, two head-to-tail condensation reactions catalyzed by the product of gene ispA ultimately produce FPP. First, geranyl diphosphate (GPP) is formed from the condensation of DMAPP and IPP, then another IPP molecule is added to GPP to form FPP. The isoprenyl chain is further elongated as shown in the linked pathways.

Reviews: [Meganathan01] and Meganathan, R. and O. Kwon (2009) "Biosynthesis of Menaquinone (Vitamin K2) and Ubiquinone (Coenzyme Q)" EcoSal [ECOSAL]

Superpathways: polyisoprenoid biosynthesis (E. coli)

Created 27-Feb-2006 by Tissier C, TAIR
Last-Curated 25-Mar-2013 by Fulcher C, SRI International


ECOSAL: "Escherichia coli and Salmonella: Cellular and Molecular Biology." Online edition.

Meganathan01: Meganathan R (2001). "Ubiquinone biosynthesis in microorganisms." FEMS Microbiol Lett 203(2);131-9. PMID: 11583838

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bonanno01: Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK (2001). "Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis." Proc Natl Acad Sci U S A 98(23);12896-901. PMID: 11698677

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Carrigan03: Carrigan CN, Poulter CD (2003). "Zinc is an essential cofactor for type I isopentenyl diphosphate:dimethylallyl diphosphate isomerase." J Am Chem Soc 125(30);9008-9. PMID: 15369345

deRuyck06: de Ruyck J, Durisotti V, Oudjama Y, Wouters J (2006). "Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography." J Biol Chem 281(26);17864-9. PMID: 16617181

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dozier12: Dozier JK, Distefano MD (2012). "An enzyme-coupled continuous fluorescence assay for farnesyl diphosphate synthases." Anal Biochem 421(1);158-63. PMID: 22085443

Durbecq01: Durbecq V, Sainz G, Oudjama Y, Clantin B, Bompard-Gilles C, Tricot C, Caillet J, Stalon V, Droogmans L, Villeret V (2001). "Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase." EMBO J 20(7);1530-7. PMID: 11285217

Fujisaki05: Fujisaki S, Takahashi I, Hara H, Horiuchi K, Nishino T, Nishimura Y (2005). "Disruption of the structural gene for farnesyl diphosphate synthase in Escherichia coli." J Biochem (Tokyo) 137(3);395-400. PMID: 15809342

Fujisaki86: Fujisaki S, Nishino T, Katsuki H (1986). "Isoprenoid synthesis in Escherichia coli. Separation and partial purification of four enzymes involved in the synthesis." J Biochem (Tokyo) 1986;99(5);1327-37. PMID: 3519603

Fujisaki89: Fujisaki S, Nishino T, Katsuki H, Hara H, Nishimura Y, Hirota Y (1989). "Isolation and characterization of an Escherichia coli mutant having temperature-sensitive farnesyl diphosphate synthase." J Bacteriol 1989;171(10);5654-8. PMID: 2676985

Fujisaki90: Fujisaki S, Hara H, Nishimura Y, Horiuchi K, Nishino T (1990). "Cloning and nucleotide sequence of the ispA gene responsible for farnesyl diphosphate synthase activity in Escherichia coli." J Biochem (Tokyo) 1990;108(6);995-1000. PMID: 2089044

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hahn99: Hahn FM, Hurlburt AP, Poulter CD (1999). "Escherichia coli open reading frame 696 is idi, a nonessential gene encoding isopentenyl diphosphate isomerase." J Bacteriol 1999;181(15);4499-504. PMID: 10419945

Harada09: Harada H, Misawa N (2009). "Novel approaches and achievements in biosynthesis of functional isoprenoids in Escherichia coli." Appl Microbiol Biotechnol 84(6);1021-31. PMID: 19672590

Hemmi98: Hemmi H, Ohnuma S, Nagaoka K, Nishino T (1998). "Identification of genes affecting lycopene formation in Escherichia coli transformed with carotenoid biosynthetic genes: candidates for early genes in isoprenoid biosynthesis." J Biochem (Tokyo) 123(6);1088-96. PMID: 9603997

Henry09: Henry O, Lopez-Gallego F, Agger SA, Schmidt-Dannert C, Sen S, Shintani D, Cornish K, Distefano MD (2009). "A versatile photoactivatable probe designed to label the diphosphate binding site of farnesyl diphosphate utilizing enzymes." Bioorg Med Chem 17(13);4797-805. PMID: 19447628

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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