MetaCyc Pathway: citrate lyase activation
Inferred from experiment

Enzyme View:

Pathway diagram: citrate lyase activation

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: BiosynthesisCofactors, Prosthetic Groups, Electron Carriers Biosynthesis

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 holo form by the covalent binding of the prosthetic group 2'-(5''-phosphoribosyl)-3'-dephospho-CoA to a serine residue. This prosthetic group is very unusual and the only other enzyme known to use it is malonate decarboxylase.

The synthesis and attachment of the prosthetic group are catalyzed by two different enzymes. The first step, catalyzed by EC, triphosphoribosyl-dephospho-CoA synthase is the formation of an unusual α-1,2-glycosidic linkage between ATP and dephospho-CoA, forming the prosthetic group and releaing adenine [Schneider00]. In the second step, catalyzed by EC, citrate lyase holo-[acyl-carrier protein] synthase, the group is transferred to the apo-[acp] protein, generating the holo-[acp] form [Schneider02a].

The holo form is still not active - in order to be fully active, the prosthetic group needs to be acetylated. The most common enzyme performing the acetylation is EC, [citrate (pro-3S)-lyase] ligase, which uses acetate as the donor [Schmellenkamp74]. A different enzyme, EC, deacetyl-[citrate-(pro-3S)-lyase] S-acetyltransferase, that uses S-acetyl phosphopantetheine as the acetyl donor, has been characterized from the bacterium Enterobacter aerogenes [Singh73].

Another enzyme that modulates the activity of citrate lyase has been reported in the bacterium Rubrivivax gelatinosus. That enzyme, EC, citrate-lyase deacetylase, converts the active acetyl form back into the inactive thiol form by removal of its acetyl groups [Giffhorn80].

Unification Links: EcoCyc:P2-PWY

Created 08-Nov-2000 by Pellegrini-Toole A, Marine Biological Laboratory
Revised 12-Feb-2008 by Caspi R, SRI International
Revised 01-Oct-2013 by Caspi R, SRI International


Giffhorn80: Giffhorn F, Rode H, Kuhn A, Gottschalk G (1980). "Citrate lyase deacetylase of Rhodopseudomonas gelatinosa. Isolation of the enzyme and studies on the inhibition by L-glutamate." Eur J Biochem 111(2);461-71. PMID: 7460909

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

Schmellenkamp74: Schmellenkamp H, Eggerer H (1974). "Mechanism of enzymic acetylation of des-acetyl citrate lyase." Proc Natl Acad Sci U S A 71(5);1987-91. PMID: 4365579

Schneider00: Schneider K, Dimroth P, Bott M (2000). "Biosynthesis of the prosthetic group of citrate lyase." Biochemistry 2000;39(31);9438-50. PMID: 10924139

Schneider00a: 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

Schneider02a: Schneider K, Kastner CN, Meyer M, Wessel M, Dimroth P, Bott M (2002). "Identification of a gene cluster in Klebsiella pneumoniae which includes citX, a gene required for biosynthesis of the citrate lyase prosthetic group." J Bacteriol 2002;184(9);2439-46. PMID: 11948157

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

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

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

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

Giffhorn75: Giffhorn F, Gottschalk G (1975). "Inactivation of citrate lyase from Rhodopseudomonas gelatinosa by a specific deacetylase and inhibition of this inactivation by L-(+1-glutamate." J Bacteriol 124(3);1052-61. PMID: 356

Giffhorn81: Giffhorn F, Zimmermann T, Kuhn A (1981). "Substrate specificity of citrate lyase deacetylase of Rhodopseudomonas gelatinosa and Rhodopseudomonas palustris." J Bacteriol 147(2);463-70. PMID: 6167565

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."

Hoenke00: Hoenke S, Wild MR, Dimroth P (2000). "Biosynthesis of triphosphoribosyl-dephospho-coenzyme A, the precursor of the prosthetic group of malonate decarboxylase." Biochemistry 39(43);13223-32. PMID: 11052675

Hoenke00a: Hoenke S, Schmid M, Dimroth P (2000). "Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases." Biochemistry 39(43);13233-40. PMID: 11052676

Hoenke97: Hoenke S, Schmid M, Dimroth P (1997). "Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli." Eur J Biochem 246(2);530-8. PMID: 9208947

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

Mootz01: Mootz HD, Finking R, Marahiel MA (2001). "4'-phosphopantetheine transfer in primary and secondary metabolism of Bacillus subtilis." J Biol Chem 276(40);37289-98. PMID: 11489886

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 Pathway Tools version 19.5 (software by SRI International) on Tue Dec 1, 2015, biocyc12.