Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: 4-hydroxybenzoate octaprenyltransferase



Gene: ubiA Accession Numbers: EG11370 (EcoCyc), b4040, ECK4032

Synonyms: sdgG?, cyr

Regulation Summary Diagram: ?

Summary:
4-Hydroxybenzoate octaprenyltransferase is the second enzyme in the pathway of ubiquinone biosynthesis. It is responsible for the prenylation of 4-hydroxybenzoate using a polyprenyldiphosphate as a side chain precursor.

UbiA is an inner membrane protein with seven predicted transmembrane domains. The C terminus is located in the periplasm [Daley05]. Earlier work experimentally localized UbiA to the membrane fraction [Young72, Melzer94].

The structure of the enzyme and its active site have been modelled [Brauer04]. In subsequent work a 3D structural model was developed that places UbiA in SCOP family 48 583. The model was experimentally supported by site-directed mutagenesis studies [Brauer08].

ubiA mutants can grow on glucose as the sole source of carbon, but can not grow on succinate [Cox68, Young72, Wu93]. A ubiA- mutant grows more slowly on glucose and accumulates acetate and lactate [Wallace77].

The sdgG10 mutation, which suppresses a conditional mutation in dnaG (DNA primase), has been localized to either the ubiC, ubiA or yjbI gene [Britton97].

ubiA is one of a network of genes believed to play a role in promoting the stress-induced mutagenesis (SIM) response of E. coli K-12 [Al12].

Reviews: [Meganathan01a, Meganathan01]

Gene Citations: [Nichols92, Heide93]

Locations: inner membrane

Map Position: [4,251,039 -> 4,251,911] (91.62 centisomes)
Length: 873 bp / 290 aa

Molecular Weight of Polypeptide: 32.512 kD (from nucleotide sequence), 32 kD (experimental) [Siebert92 ]

pI: 9.16

Unification Links: ASAP:ABE-0013229 , CGSC:50 , EchoBASE:EB1344 , EcoGene:EG11370 , EcoliWiki:b4040 , OU-Microarray:b4040 , PortEco:ubiA , PR:PRO_000024155 , Protein Model Portal:P0AGK1 , RefSeq:NP_418464 , RegulonDB:EG11370 , String:511145.b4040 , UniProt:P0AGK1

Relationship Links: InterPro:IN-FAMILY:IPR000537 , InterPro:IN-FAMILY:IPR006370 , Pfam:IN-FAMILY:PF01040 , Prosite:IN-FAMILY:PS00943

In Paralogous Gene Group: 567 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006744 - ubiquinone biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA01, Young72]
Molecular Function: GO:0008412 - 4-hydroxybenzoate octaprenyltransferase activity Inferred from experiment [Melzer94]
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups Inferred from experiment [Melzer94]
GO:0004659 - prenyltransferase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell structure membrane
metabolism biosynthesis of building blocks cofactors, small molecule carriers menaquinone, ubiquinone
metabolism energy metabolism, carbon aerobic respiration

Essentiality data for ubiA knockouts: ?

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

Credits:
Curated 10-Jul-2007 by Keseler I , SRI International
Last-Curated ? 27-Mar-2013 by Fulcher C , SRI International


Enzymatic reaction of: 4-hydroxybenzoate octaprenyltransferase

Synonyms: 4-HB polyprenyltransferase, polyprenyldiphosphate:4-hydroxybenzoate polyprenyltransferase, 4-hydroxybenzoate polyprenyl transferase

EC Number: 2.5.1.39

all-trans-octaprenyl diphosphate + 4-hydroxybenzoate <=> 3-octaprenyl-4-hydroxybenzoate + 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.

Alternative Substrates for all-trans-octaprenyl diphosphate: all-trans-nonaprenyl diphosphate [elHachimi74 , Melzer94 ] , (2E,6E)-farnesyl diphosphate [elHachimi74 , Melzer94 ] , geranyl diphosphate [Melzer94 ]

In Pathways: superpathway of chorismate metabolism , superpathway of ubiquinol-8 biosynthesis (prokaryotic) , ubiquinol-8 biosynthesis (prokaryotic)

Summary:
The pH optimum was determined using geranyl-PP as the substrate. Apparent Km values for geranyl-PP, farnesyl-PP, and solanesyl-PP are 255, 22, and 31 µM, respectively. The enzyme appears to be specific for the all-trans-polyprenyldiphosphates [Melzer94].

In addition to a lack of specificity for polyprenyl substrates, the enzyme can also accept a wide variety of benzoic acid derivatives and related compounds as substrates [Wessjohann96].

Cofactors or Prosthetic Groups: Mg2+ [Comment 2, Melzer94, Young72]

Activators (Unknown Mechanism): CHAPS [Melzer94]

Inhibitors (Unknown Mechanism): deoxycholate [Melzer94] , Tween 80 [Melzer94] , Triton X-100 [Melzer94]

pH(opt): 7.8 [Melzer94]


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 23 -> 43
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 46 -> 66
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 100 -> 120
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 141 -> 161
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 163 -> 183
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 213 -> 233
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 234 -> 254
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 268 -> 288
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b4040 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11370; confirmed by SwissProt match.


References

Al12: Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM (2012). "Identity and function of a large gene network underlying mutagenic repair of DNA breaks." Science 338(6112);1344-8. PMID: 23224554

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

Brauer04: Brauer L, Brandt W, Wessjohann LA (2004). "Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase ( ubiA transferase) and characterization of potential active sites." J Mol Model 10(5-6);317-27. PMID: 15597200

Brauer08: Brauer L, Brandt W, Schulze D, Zakharova S, Wessjohann L (2008). "A structural model of the membrane-bound aromatic prenyltransferase UbiA from E. coli." Chembiochem 9(6);982-92. PMID: 18338424

Britton97: Britton RA, Lupski JR (1997). "Isolation and characterization of suppressors of two Escherichia coli dnaG mutations, dnaG2903 and parB." Genetics 145(4);867-75. PMID: 9093842

Cox68: Cox GB, Gibson F, Pittard J (1968). "Mutant strains of Escherichia coli K-12 unable to form ubiquinone." J Bacteriol 95(5);1591-8. PMID: 4870277

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

elHachimi74: el-Hachimi Z, Samuel O, Azerad R (1974). "Biochemical study on ubiquinone biosynthesis in Escherichia coli : I. Specificity of para hydroxybenzoate polyprenyltransferase." Biochimie 1974;56(9);1239-47. PMID: 4615746

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Heide93: Heide L, Melzer M, Siebert M, Bechthold A, Schroder J, Severin K (1993). "Clarification of the Escherichia coli genetic map in the 92-minute region containing the ubiCA operon and the plsB, dgk, lexA, and dinF genes." J Bacteriol 1993;175(17);5728-9. PMID: 8366060

Meganathan01: Meganathan R (2001). "Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms." Vitam Horm 61;173-218. PMID: 11153266

Meganathan01a: Meganathan R (2001). "Ubiquinone biosynthesis in microorganisms." FEMS Microbiol Lett 203(2);131-9. PMID: 11583838

Melzer94: Melzer M, Heide L (1994). "Characterization of polyprenyldiphosphate: 4-hydroxybenzoate polyprenyltransferase from Escherichia coli." Biochim Biophys Acta 1994;1212(1);93-102. PMID: 8155731

Nichols92: Nichols BP, Green JM (1992). "Cloning and sequencing of Escherichia coli ubiC and purification of chorismate lyase." J Bacteriol 1992;174(16);5309-16. PMID: 1644758

Siebert92: Siebert M, Bechthold A, Melzer M, May U, Berger U, Schroder G, Schroder J, Severin K, Heide L (1992). "Ubiquinone biosynthesis. Cloning of the genes coding for chorismate pyruvate-lyase and 4-hydroxybenzoate octaprenyl transferase from Escherichia coli." FEBS Lett 307(3);347-50. PMID: 1644192

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."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Wallace77: Wallace BJ, Young IG (1977). "Role of quinones in electron transport to oxygen and nitrate in Escherichia coli. Studies with a ubiA- menA- double quinone mutant." Biochim Biophys Acta 461(1);84-100. PMID: 195602

Wessjohann96: Wessjohann L, Sontag B (1996). "Prenylation of Benzoic Acid Derivatives Catalyzed by a Transferase fromEscherichia coli Overproduction: Method Development and Substrate Specificity." Angewandte Chemie International Edition in English 35(15);1697-1699.

Wu93: Wu G, Williams HD, Gibson F, Poole RK (1993). "Mutants of Escherichia coli affected in respiration: the cloning and nucleotide sequence of ubiA, encoding the membrane-bound p-hydroxybenzoate:octaprenyltransferase." J Gen Microbiol 1993;139 ( Pt 8);1795-805. PMID: 8409922

Young72: Young IG, Leppik RA, Hamilton JA, Gibson F (1972). "Biochemical and genetic studies on ubiquinone biosynthesis in Escherichia coli K-12:4-hydroxybenzoate octaprenyltransferase." J Bacteriol 110(1);18-25. PMID: 4552989

Other References Related to Gene Regulation

Kwon05: Kwon O, Druce-Hoffman M, Meganathan R (2005). "Regulation of the Ubiquinone (Coenzyme Q) Biosynthetic Genes ubiCA in Escherichia coli." Curr Microbiol 50(4);180-9. PMID: 15902464

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

Soballe97: Soballe B, Poole RK (1997). "Aerobic and anaerobic regulation of the ubiCA operon, encoding enzymes for the first two committed steps of ubiquinone biosynthesis in Escherichia coli." FEBS Lett 414(2);373-6. PMID: 9315722


Report Errors or Provide Feedback
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 18.5 on Sun Nov 23, 2014, biocyc14.