Escherichia coli K-12 substr. MG1655 Enzyme: octaprenyl diphosphate synthase

Gene: ispB Accession Numbers: EG10017 (EcoCyc), b3187, ECK3176

Synonyms: cel, yhbD

Regulation Summary Diagram: ?

Regulation summary diagram for ispB

Subunit composition of octaprenyl diphosphate synthase = [IspB]2
         octaprenyl diphosphate synthase = IspB

Octaprenyl diphosphate (OPP) synthase catalyzes the condensation reactions resulting in the formation of OPP, the isoprenoid side chain of ubiquinone-8. To generate OPP, five isopentenyl diphosphate molecules are sequentially added to farnesyl diphosphate with trans stereochemistry [Fujisaki86, Asai94].

Residues that are important for determination of isoprenoid chain length have been identified by mutagenesis. Dimerization of the enzyme appears to play a role in chain length determination [Kainou01].

Various detergents enhance the activity of the enzyme, which is thought to be limited by slow product release. Steady-state and pre-steady-state experiments were performed to obtain kinetic data [Pan02].

ispB is essential for growth in E. coli [Okada97, Baba06].

In comparative studies of reaction mechanisms, E. coli octaprenyl diphosphate synthase, a trans-prenyltransferase, was found to use a sequential ionization-condensation-elimination mechanism involving a farnesyl carbocation intermediate. In contrast, undecaprenyl diphosphate synthase, a cis-prenyltransferase that utilizes the same substrate, was found to use a concerted mechanism [Lu09]. Subsequent site-directed mutagenesis studies probed the roles of active site amino acids in the catalytic mechanism of IspB [Chang12].

A preliminary X-ray diffraction analysis of the E. coli enzyme at 2.2 Å resolution has been reported. The crystal contained one homodimer per asymmetric unit [Li13a].

In an E. coli strain engineered to produce coenzyme Q10, deletion of endogenous ispB and use of a heterologous dps gene expression system for overexpression of decaprenyl diphosphate synthase enhanced coenzyme Q10 production [Choi09].

Expression of the Schizosaccharomyces pombe genes dlp1 and dps1 encoding heteromeric decaprenyl diphosphate synthase in an E. coli strain containing an ispBR321A mutation resulted in recovery of the thermo-sensitive growth of this mutant. It also restored both IspB activity and coenzyme Q8 production. Evidence suggested that IspB interacts with Dlp1 or Dps1 to form heteromeric high-molecular weight complexes that stabilize IspB activity. The evolutionary implications were discussed [Cui10].

cel: "crtE-like gene" [Jeong93]

Locations: cytosol

Map Position: [3,331,732 -> 3,332,703] (71.81 centisomes, 259°)
Length: 972 bp / 323 aa

Molecular Weight of Polypeptide: 35.217 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010474 , CGSC:35712 , EchoBASE:EB0017 , EcoGene:EG10017 , EcoliWiki:b3187 , Mint:MINT-7384996 , ModBase:P0AD57 , OU-Microarray:b3187 , PortEco:ispB , PR:PRO_000023035 , Pride:P0AD57 , Protein Model Portal:P0AD57 , RefSeq:NP_417654 , RegulonDB:EG10017 , SMR:P0AD57 , String:511145.b3187 , UniProt:P0AD57

Relationship Links: InterPro:IN-FAMILY:IPR000092 , InterPro:IN-FAMILY:IPR008949 , InterPro:IN-FAMILY:IPR017446 , Panther:IN-FAMILY:PTHR12001 , Pfam:IN-FAMILY:PF00348 , Prosite:IN-FAMILY:PS00444 , Prosite:IN-FAMILY:PS00723

In Paralogous Gene Group: 124 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006744 - ubiquinone biosynthetic process Inferred from experiment [Kainou01]
GO:0016094 - polyprenol biosynthetic process Inferred from experiment [Kainou01]
GO:0008299 - isoprenoid biosynthetic process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0004659 - prenyltransferase activity Inferred from experiment [Pan02]
GO:0005515 - protein binding Inferred from experiment [Cui10]
GO:0042802 - identical protein binding Inferred from experiment [Cui10]
GO:0042803 - protein homodimerization activity Inferred from experiment [Li13a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers menaquinone, ubiquinone

Essentiality data for ispB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Created 13-Sep-2006 by Keseler I , SRI International
Curated 17-Jul-2007 by Keseler I , SRI International
Last-Curated ? 26-Mar-2013 by Fulcher C , SRI International

Enzymatic reaction of: (E)-heptaprenyl-diphosphate:isopentenyl-diphosphate octaprenyltranstransferase (octaprenyl diphosphate synthase)

Synonyms: octaprenyl pyrophosphate synthase, OPP synthase

EC Number:

(2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate <=> all-trans-octaprenyl diphosphate + 5 diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of chorismate metabolism , superpathway of ubiquinol-8 biosynthesis (prokaryotic) , polyisoprenoid biosynthesis (E. coli) , superpathway of menaquinol-8 biosynthesis I , octaprenyl diphosphate biosynthesis

The enzymatic reaction was stated to be irreversible, although this was not experimentally demonstrated [Pan02].

Cofactors or Prosthetic Groups: Mg2+ [Fujisaki86]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
(2E,6E)-farnesyl diphosphate
(2E,6E)-farnesyl diphosphate
[Chang12, BRENDA14]
isopentenyl diphosphate
[Chang12, BRENDA14]
isopentenyl diphosphate
[Pan02, BRENDA14]

pH(opt): 7-7.5 [Fujisaki86]

Sequence Features

Protein sequence of octaprenyl diphosphate synthase with features indicated

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 45
UniProt: Isopentenyl diphosphate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 48
UniProt: Isopentenyl diphosphate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 77
UniProt: Isopentenyl diphosphate; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 84
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 88
UniProt: Magnesium 1; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 93
UniProt: Polyprenyl diphosphate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 94
UniProt: Isopentenyl diphosphate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 170
UniProt: Polyprenyl diphosphate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 171
UniProt: Polyprenyl diphosphate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 208
UniProt: Polyprenyl diphosphate; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 211
UniProt: Magnesium 3; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3187 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10017; confirmed by SwissProt match.


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."

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

GOA01: 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

Li13a: 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

Okada97: 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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Wed Aug 5, 2015, BIOCYC13A.