Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

MetaCyc Pathway: octaprenyl diphosphate biosynthesis

Enzyme View:

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Biosynthesis Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis Polyprenyl Biosynthesis

Some taxa known to possess this pathway include ? : Aeromonas hydrophila , Arthrobacter nicotianae , Arthrobacter ureafaciens , Azotobacter vinelandii , Bordetella pertussis , Brevibacterium iodinum , Brevibacterium linens , Brevibacterium sterolicum , Corynebacterium diphtheriae , Corynebacterium flavescens , Corynebacterium kutscheri , Corynebacterium pseudotuberculosis , Corynebacterium renale , Corynebacterium ulcerans , Corynebacterium xerosis , Cupriavidus necator , Deinococcus radiodurans , Ectothiorhodospira haloalkaliphila , Enterobacter aerogenes , Escherichia coli K-12 substr. MG1655 , Halobacterium salinarum , Halobacterium sp. NCIMB 763 , Halococcus morrhuae , Haloferax volcanii , Halorubrum saccharovorum , Halorubrum trapanicum , Lactobacillus mali , Micrococcus luteus , Nocardia asteroides , Nocardia brasiliensis , Nocardia farcinica , Nocardia transvalensis , Nocardia vaccinii , Pimelobacter simplex , Proteus mirabilis , Proteus vulgaris , Rhodococcus corynebacterioides , Rhodococcus erythropolis , Rhodococcus fascians , Rhodococcus hoagii , Rhodococcus rhodnii , Rhodococcus rhodochrous , Rhodococcus ruber , Rubrivivax gelatinosus , Salinivibrio costicola , Serratia marcescens , Staphylococcus aureus , Stenotrophomonas maltophilia , Streptomyces gardneri , Thermus aquaticus , Thermus thermophilus , Virgibacillus pantothenticus , Xanthomonas campestris , Xanthomonas citri , Xanthomonas oryzae , Yersinia pseudotuberculosis

Expected Taxonomic Range: Archaea , Bacteria , Eukaryota

Summary:
In this pathway multiple units of isopentenyl diphosphate (IPP) undergo a series of polymerizations to form a polyisoprenoid chain.

The sequential addition of isoprenyl units to (2E,6E)-farnesyl diphosphate is performed by polyprenyl diphosphate synthase enzymes such as the Escherichia coli enzyme octaprenyl diphosphate synthase.

Additional isoprenoid units are added to a maximal length that is determined by the specific enzyme. Most organisms generate polyprenyl chains of predominantly one length. Once completed, the polyprenyl chain is incorporated into other molecules, such as quinones. The enzyme that attaches the polyprenyl chain to the quinone precursor molecule does not have a preference towards a particular length. Thus, the length of the polyprenyl chain in the mature quinone molecule is determined by the predominant polyprenyl diphosphate synthase enzyme of the organism.

In most organisms there is one type of a predominant quinone, with a specific polyprenyl chain length. However, most organisms also have minor amounts of quinones with a different polyprenyl chain length. Quinones containing chains of 8 prenyl units are found in all kingdoms of life. They are particularly common among the Archaea (in the form of menaquinone-8) and the Enterobacteriaceae. For a review detailing the distribution of polyprenyl chain length in different bacteria, see [Collins81].

In Escherichia coli K-12 the initial addition of two isoprenyl units to form (2E,6E)-farnesyl diphosphate is catalyzed by geranyl diphosphate synthase / farnesyl diphosphate synthase, encoded by ispA. Additional isoprenoid units are added sequentially to a maximal length of 8 units by octaprenyl diphosphate synthase, encoded by ispB.

Superpathways: superpathway of menaquinol-8 biosynthesis I , superpathway of demethylmenaquinol-8 biosynthesis , superpathway of ubiquinol-8 biosynthesis (prokaryotic) , superpathway of menaquinol-8 biosynthesis II , polyisoprenoid biosynthesis (E. coli) , superpathway of chorismate metabolism

Unification Links: EcoCyc:PWY-5783

Credits:
Created 05-Feb-2008 by Caspi R , SRI International


References

Collins81: Collins MD, Jones D (1981). "Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication." Microbiol Rev 45(2);316-54. PMID: 7022156

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

Asai94: Asai K, Fujisaki S, Nishimura Y, Nishino T, Okada K, Nakagawa T, Kawamukai M, Matsuda H (1994). "The identification of Escherichia coli ispB (cel) gene encoding the octaprenyl diphosphate synthase." Biochem Biophys Res Commun 202(1);340-5. PMID: 8037730

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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Chang12: Chang KM, Chen SH, Kuo CJ, Chang CK, Guo RT, Yang JM, Liang PH (2012). "Roles of amino acids in the Escherichia coli octaprenyl diphosphate synthase active site probed by structure-guided site-directed mutagenesis." Biochemistry 51(16);3412-9. PMID: 22471615

Choi09: Choi JH, Ryu YW, Park YC, Seo JH (2009). "Synergistic effects of chromosomal ispB deletion and dxs overexpression on coenzyme Q(10) production in recombinant Escherichia coli expressing Agrobacterium tumefaciens dps gene." J Biotechnol 144(1);64-9. PMID: 19409940

Cui10: Cui TZ, Kaino T, Kawamukai M (2010). "A subunit of decaprenyl diphosphate synthase stabilizes octaprenyl diphosphate synthase in Escherichia coli by forming a high-molecular weight complex." FEBS Lett 584(4);652-6. PMID: 20051244

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

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

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

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jeong93: Jeong JH, Kitakawa M, Isono S, Isono K (1993). "Cloning and nucleotide sequencing of the genes, rpIU and rpmA, for ribosomal proteins L21 and L27 of Escherichia coli." DNA Seq 4(1);59-67. PMID: 8312607

Kainou01: Kainou T, Okada K, Suzuki K, Nakagawa T, Matsuda H, Kawamukai M (2001). "Dimer formation of octaprenyl-diphosphate synthase (IspB) is essential for chain length determination of ubiquinone." J Biol Chem 276(11);7876-83. PMID: 11108713

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Li13: Li X, Han X, Ko TP, Chen CC, Zhu Z, Hua E, Guo RT, Huang CH (2013). "Preliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase from Escherichia coli." Acta Crystallogr Sect F Struct Biol Cryst Commun 69(Pt 3);328-31. PMID: 23519815

Lu09: Lu YP, Liu HG, Liang PH (2009). "Different reaction mechanisms for cis- and trans-prenyltransferases." Biochem Biophys Res Commun 379(2);351-5. PMID: 19103164

Ohnuma91: Ohnuma S, Koyama T, Ogura K (1991). "Purification of solanesyl-diphosphate synthase from Micrococcus luteus. A new class of prenyltransferase." J Biol Chem 266(35);23706-13. PMID: 1748647

Ohnuma92: Ohnuma S, Koyama T, Ogura K (1992). "Chain length distribution of the products formed in solanesyl diphosphate synthase reaction." J Biochem 112(6);743-9. PMID: 1295881

Okada97a: Okada K, Minehira M, Zhu X, Suzuki K, Nakagawa T, Matsuda H, Kawamukai M (1997). "The ispB gene encoding octaprenyl diphosphate synthase is essential for growth of Escherichia coli." J Bacteriol 179(9);3058-60. PMID: 9139929

Pan02: Pan JJ, Kuo TH, Chen YK, Yang LW, Liang PH (2002). "Insight into the activation mechanism of Escherichia coli octaprenyl pyrophosphate synthase derived from pre-steady-state kinetic analysis." Biochim Biophys Acta 1594(1);64-73. PMID: 11825609

Saito81: Saito Y, Ogura K (1981). "Biosynthesis of menaquinones. Enzymatic prenylation of 1,4-dihydroxy-2-naphthoate by Micrococcus luteus membrane fractions." J Biochem 89(5);1445-52. PMID: 7275947

Showing only 20 references. To show more, press the button "Show all references".


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, biocyc14.