|Gene:||ubiC||Accession Numbers: EG11369 (EcoCyc), b4039, ECK4031|
Chorismate pyruvate lyase catalyzes the first committed step in the biosynthesis of ubiquinone, the conversion of chorismate to 4-hydroxybenzoate [Nichols92, Siebert94]. The enzyme retains and is efficiently inhibited by the product of the reaction, 4-hydroxybenzoate, which may present a control mechanism for the ubiquinone biosynthesis pathway or a mechanism for delivery of 4-hydroxybenzoate to the membrane [Gallagher01a, Holden02].
Crystal structures of the enzyme in various forms have been solved; the structures have revealed the basis for tight product binding and the structural basis for the catalytic and product release mechanisms [Gallagher01a, Smith06].
A ubiC mutant can grow on glucose as the sole source of carbon, but can not grow on malate or succinate unless 4-hydroxybenzoate is present [Cox68, Lawrence74]. Overexpression of ubiC can complement a pabC mutation, although the purified protein did not have appreciable activity with 4-amino-4-deoxychorismate as the substrate [Nichols92].
The sdgG10 mutation, which suppresses a conditional mutation in dnaG (DNA primase), has been localized to either the ubiC, ubiA or yjbI gene [Britton97].
Gene Citations: [Heide93]
|Map Position: [4,250,529 -> 4,251,026] (91.61 centisomes, 330°)||Length: 498 bp / 165 aa|
Molecular Weight of Polypeptide: 18.777 kD (from nucleotide sequence), 19 kD (experimental) [Siebert92 ]
pI: 6.45 [Siebert94]
Unification Links: ASAP:ABE-0013227 , CGSC:48 , DIP:DIP-11066N , EchoBASE:EB1343 , EcoGene:EG11369 , EcoliWiki:b4039 , Mint:MINT-1235748 , ModBase:P26602 , OU-Microarray:b4039 , PortEco:ubiC , PR:PRO_000024156 , Pride:P26602 , Protein Model Portal:P26602 , RefSeq:NP_418463 , RegulonDB:EG11369 , SMR:P26602 , String:511145.b4039 , UniProt:P26602
Relationship Links: InterPro:IN-FAMILY:IPR007440 , InterPro:IN-FAMILY:IPR028978 , PDB:Structure:1FW9 , PDB:Structure:1G1B , PDB:Structure:1G81 , PDB:Structure:1JD3 , PDB:Structure:1TT8 , PDB:Structure:1XLR , PDB:Structure:2AHC , Pfam:IN-FAMILY:PF04345
|Biological Process:||GO:0006744 - ubiquinone biosynthetic process
[UniProtGOA12, UniProtGOA11a, GOA06, GOA01a, Lawrence74]
GO:0042866 - pyruvate biosynthetic process [GOA06]
|Molecular Function:||GO:0008813 - chorismate lyase activity
[GOA06, GOA01, GOA01a, Nichols92, Lawrence74]
GO:0016829 - lyase activity [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol
GO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]
|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 enriched||Yes||37||Aerobic||6.95||Yes [Gerdes03, Comment 1]|
|LB Lennox||Yes||37||Aerobic||7||Yes [Baba06, Comment 2]|
|M9 medium with 1% glycerol||Yes||37||Aerobic||7.2||0.35||Yes [Joyce06, Comment 3]|
|MOPS medium with 0.4% glucose||Yes||37||Aerobic||7.2||0.22||Yes [Baba06, Comment 2] |
Yes [Feist07, Comment 4]
Enzymatic reaction of: chorismate lyase
Synonyms: CPL, chorismate pyruvate lyase
EC Number: 126.96.36.199
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 irreversible in the direction shown. [Siebert94]
In Pathways: 4-hydroxybenzoate biosynthesis II (microbes)
CPL appears capable of converting 4-amino-4-deoxychorismate to 4-aminobenzoate in vivo. It will not accept isochorismate as a substrate suggesting a hydroxy or amino function in the 4-position is essential for activity. [Nichols92, Siebert94]
No reverse reaction was observed using 4-hydroxybenzoate and pyruvate at concentrations up to 25 mM and 250 mM, respectively [Siebert94]. The equilibrium constant for the reaction is approximately 1037 [Tewari98].
Primary Physiological Regulators of Enzyme Activity: 4-hydroxybenzoate
pH(opt): 7.5 [Siebert94]
|Chain||2 -> 165|
Martin Peralta on Fri Oct 29, 2004:
The start site of this gene was originally assigned solely on the basis of sequence considerations (Blattner et al, 1997, PubMed: 9278503). However, it was changed because Nichols and Green, 1992, determined a 1,034-pb nucleotide sequence containing all of the E. coli ubiC gene (PMID:1644758). The demonstration is based on (a) determination of the protein size, plus (b) identification of both a plausible ribosome binding site and a promoter at an appropriate distance from the new start site.
10/20/97 Gene b4039 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11369.
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
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
Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909
Gallagher01a: Gallagher DT, Mayhew M, Holden MJ, Howard A, Kim KJ, Vilker VL (2001). "The crystal structure of chorismate lyase shows a new fold and a tightly retained product." Proteins 44(3);304-11. PMID: 11455603
Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938
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
Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394
Lawrence74: Lawrence J, Cox GB, Gibson F (1974). "Biosynthesis of ubiquinone in Escherichia coli K-12: biochemical and genetic characterization of a mutant unable to convert chorismate into 4-hydroxybenzoate." J Bacteriol 118(1);41-5. PMID: 4595202
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
Siebert94: Siebert M, Severin K, Heide L (1994). "Formation of 4-hydroxybenzoate in Escherichia coli: characterization of the ubiC gene and its encoded enzyme chorismate pyruvate-lyase." Microbiology 1994;140 ( Pt 4);897-904. PMID: 8012607
Smith06: Smith N, Roitberg AE, Rivera E, Howard A, Holden MJ, Mayhew M, Kaistha S, Gallagher DT (2006). "Structural analysis of ligand binding and catalysis in chorismate lyase." Arch Biochem Biophys 445(1);72-80. PMID: 16343413
Tewari98: Tewari YB, Chen J, Holden MJ, Houk KN, Goldberg RN (1998). "Thermodynamic and Quantum Chemical Study of the Conversion of Chorismate to (Pyruvate + 4-Hydroxybenzoate)." J Phys Chem B 102; 8634-8639.
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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