MetaCyc Pathway: citrate degradation
Inferred from experiment

Enzyme View:

Pathway diagram: citrate degradation

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/AssimilationCarboxylates Degradation

Some taxa known to possess this pathway include : Enterobacter aerogenes, Escherichia coli K-12 substr. MG1655, Klebsiella pneumoniae, Rubrivivax gelatinosus

Expected Taxonomic Range: Bacteria

Citrate lyase is an anaerobic enzyme that catalyzes the cleavage of citrate to acetate and oxaloacetate [Nilekani83] (see citrate degradation). Because the citrate molecule is very stable, it has to be activated by forming a thioester bond with the enzyme before cleavage can take place.

The enzyme is a complex of three subunits (in a 6:6:6 configuration), one of them a dedicated acyl carrier protein (acp). The acp protein is synthesized in an apo form, and is converted to its fully active form in two steps - first, a holo form is generated by the covalent binding of the prosthetic group 2'-(5''-phosphoribosyl)-3'-dephospho-CoA to a serine residue. Next, the holo form is acetylated, either by EC, [citrate (pro-3S)-lyase] ligase, which uses acetate as the donor, or by EC, deacetyl-[citrate-(pro-3S)-lyase] S-acetyltransferase, that uses S-acetyl phosphopantetheine as the acetyl donor (see citrate lyase activation).

The α subunit of the citrate lyase is EC, citrate CoA-transferase, an enzyme that catalyzes the exchange of the bound acetyl group with a citrate molecule, generating a citryl-[holo citrate lyase acyl-carrier protein] and releasing an acetate molecule. The β subunit, EC, citryl-CoA lyase, catalyzes the subsequent step, cleaving the bound citryl group, releasing oxaloacetate and regenerating an acetyl-[holo citrate lyase acyl-carrier protein]. Since the active form is regenrated, the enzyme can continuously catalyze the cleavage reaction.

Genes complementary to the bacterial citrate lyase β subunit have been identified in the mouse and human genomes [Morikawa01]. The physiological role of these genes in eukaryotes is not known yet.

The sum of this pathway is described by EC, citrate (pro-3S)-lyase: citrate → acetate + oxaloacetate

Unification Links: EcoCyc:PWY-6038

Created 12-Sep-2008 by Caspi R, SRI International
Revised 01-Oct-2013 by Caspi R, SRI International


Morikawa01: Morikawa J, Nishimura Y, Uchida A, Tanaka T (2001). "Molecular cloning of novel mouse and human putative citrate lyase beta-subunit." Biochem Biophys Res Commun 289(5);1282-6. PMID: 11741334

Nilekani83: Nilekani S, SivaRaman C (1983). "Purification and properties of citrate lyase from Escherichia coli." Biochemistry 1983;22(20);4657-63. PMID: 6354265

Singh73: Singh M, Bottger B, Stewart C, Brooks GC, Srere PA (1973). "S-acetyl phosphopantetheine: deacetyl citrate lyase S-acetyl transferase from Klebsiella aerogenes." Biochem Biophys Res Commun 53(1);1-9. PMID: 4741546

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Beyreuther78: Beyreuther K, Bohmer H, Dimroth P (1978). "Amino-acid sequence of citrate-lyase acyl-carrier protein from Klebsiella aerogenes." Eur J Biochem 87(1);101-10. PMID: 352686

Bott94: Bott M, Dimroth P (1994). "Klebsiella pneumoniae genes for citrate lyase and citrate lyase ligase: localization, sequencing, and expression." Mol Microbiol 14(2);347-56. PMID: 7830578

Clark90: Clark DP (1990). "Molybdenum cofactor negative mutants of Escherichia coli use citrate anaerobically." FEMS Microbiol Lett 1990;55(3);245-9. PMID: 2182384

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

Dimroth75: Dimroth P, Eggerer H (1975). "Isolation of subunits of citrate lyase and characterization of their function in the enzyme complex." Proc Natl Acad Sci U S A 72(9);3458-62. PMID: 1060145

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Hupperich90: Hupperich M, Henschen A, Eggerer H (1990). "Citrate lyase from Klebsiella pneumoniae. The complete primary structure of the acyl lyase subunit." Eur J Biochem 192(1);161-6. PMID: 2205500

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Quentmeier87: Quentmeier A, Holzenburg A, Mayer F, Antranikian G (1987). "Reevaluation of citrate lyase from Escherichia coli." Biochim Biophys Acta 1987;913(1);60-5. PMID: 3555623

Schneider00: Schneider K, Dimroth P, Bott M (2000). "Identification of triphosphoribosyl-dephospho-CoA as precursor of the citrate lyase prosthetic group." FEBS Lett 2000;483(2-3);165-8. PMID: 11042274

Schneider00a: Schneider K, Dimroth P, Bott M (2000). "Biosynthesis of the prosthetic group of citrate lyase." Biochemistry 2000;39(31);9438-50. PMID: 10924139

Singh76: Singh M, Srere PA (1976). "Subunit and chemical composition of citrate lyase from Klebsiella pneumoniae." J Biol Chem 251(10);2911-5. PMID: 773936

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."

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.5 on Thu Nov 26, 2015, BIOCYC13B.