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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: [Meganathan01, Meganathan01a]

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, UniProtGOA11a, 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 [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, 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). "Ubiquinone biosynthesis in microorganisms." FEMS Microbiol Lett 203(2);131-9. PMID: 11583838

Meganathan01a: Meganathan R (2001). "Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms." Vitam Horm 61;173-218. PMID: 11153266

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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords 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


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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 18.5 on Fri Dec 19, 2014, BIOCYC13A.