Escherichia coli K-12 substr. MG1655 Enzyme: chorismate lyase

Gene: ubiC Accession Numbers: EG11369 (EcoCyc), b4039, ECK4031

Synonyms: sdgG?

Regulation Summary Diagram: ?

Regulation summary diagram for ubiC

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 [Gallagher01, 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 [Gallagher01, 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].

Reviews: [Meganathan01, Meganathan01a]

Gene Citations: [Heide93]

Locations: cytosol

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

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for ubiC

GO Terms:

Biological Process: GO:0006744 - ubiquinone biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01, Lawrence74]
GO:0042866 - pyruvate biosynthetic process Inferred by computational analysis [GOA06]
Molecular Function: GO:0008813 - chorismate lyase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Nichols92, Lawrence74]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Nichols92]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

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

Essentiality data for ubiC knockouts: ?

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]

Last-Curated ? 01-Jun-2012 by Fulcher C , SRI International

Enzymatic reaction of: chorismate lyase

Synonyms: CPL, chorismate pyruvate lyase

EC Number:

chorismate <=> 4-hydroxybenzoate + pyruvate

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].

Inhibitors (Competitive): vanillate [Holden02] , 4-hydroxybenzaldehyde [Holden02] , 3-(carboxymethylaminomethyl)-4-hydroxybenzoate [Holden02] , 4-hydroxybenzoate [Holden02, Comment 5]

Primary Physiological Regulators of Enzyme Activity: 4-hydroxybenzoate

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Nichols92, BRENDA14]
28.0, 29.0
1.5, 1.7
0.054, 0.061, 0.052, 0.059
[Holden02, BRENDA14]

pH(opt): 7.5 [Siebert94]

Sequence Features

Protein sequence of chorismate lyase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Cleavage of the initiating methionine was confirmed by N-terminal sequencing of the purified protein [Nichols92].
Chain 2 -> 165
UniProt: Chorismate--pyruvate lyase;
Amino-Acid-Sites-That-Bind 35
UniProt: Substrate; via amide nitrogen.
Amino-Acid-Sites-That-Bind 77
UniProt: Substrate.
Mutagenesis-Variant 91
[Smith06, UniProt11a]
UniProt: Increases the inhibition by product by about 40%. No effect on substrate affinity.
Amino-Acid-Sites-That-Bind 115
UniProt: Substrate; via amide nitrogen.
Mutagenesis-Variant 156
[Siebert94, UniProt11a]
UniProt: Loss of activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

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

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

Gallagher01: 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

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Holden02: Holden MJ, Mayhew MP, Gallagher DT, Vilker VL (2002). "Chorismate lyase: kinetics and engineering for stability." Biochim Biophys Acta 1594(1);160-7. PMID: 11825618

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

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

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

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.

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

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 19.0 on Tue Oct 6, 2015, biocyc13.