|Gene:||ispB||Accession Numbers: EG10017 (EcoCyc), b3187, ECK3176|
Synonyms: cel, yhbD
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].
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 [Li13].
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]
|Map Position: [3,331,732 -> 3,332,703] (71.81 centisomes)||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)
|Biological Process:||GO:0006744 - ubiquinone biosynthetic process
GO:0016094 - polyprenol biosynthetic process [Kainou01]
GO:0008299 - isoprenoid biosynthetic process [UniProtGOA11, GOA01]
|Molecular Function:||GO:0004659 - prenyltransferase activity
GO:0005515 - protein binding [Cui10]
GO:0042802 - identical protein binding [Cui10]
GO:0042803 - protein homodimerization activity [Li13]
GO:0016740 - transferase activity [UniProtGOA11]
GO:0046872 - metal ion binding [UniProtGOA11]
|Cellular Component:||GO:0005829 - cytosol [DiazMejia09, Ishihama08]|
|MultiFun Terms:||metabolism → biosynthesis of building blocks → cofactors, small molecule carriers → menaquinone, ubiquinone|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Enzymatic reaction of: (E)-heptaprenyl-diphosphate:isopentenyl-diphosphate octaprenyltranstransferase (octaprenyl diphosphate synthase)
Synonyms: octaprenyl pyrophosphate synthase, OPP synthase
EC Number: 18.104.22.168
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].
pH(opt): 7-7.5 [Fujisaki86]
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
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
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
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
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
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