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discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
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MetaCyc Protein: citrate lyase, inactive

Synonyms: (HS)-citrate lyase, citrate lyase, thiol form, deacetyl-citrate lyase

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of citrate lyase, inactive = [(CitD)6][(CitF)6][(CitE)6]
         citrate lyase [acyl carrier protein] component = (CitD)6 (summary available)
                 citrate lyase, acyl carrier γ subunit = CitD
         citrate lyase, citrate-ACP transferase component = (CitF)6
                 citrate lyase, citrate-ACP transferase α subunit = CitF
         citrate lyase, citryl-ACP lyase component = (CitE)6
                 citrate lyase, citryl-ACP lyase β subunit = CitE

Alternative forms of citrate lyase, inactive: citrate lyase (extended summary available)

Reactions known to consume the compound:

citrate lyase activation :
[a holo citrate lyase acyl-carrier protein] + S-acetyl phosphopantetheine → an acetyl-[holo citrate lyase acyl-carrier protein] + 4'-phosphopantetheine
[a holo citrate lyase acyl-carrier protein] + acetate + ATP → an acetyl-[holo citrate lyase acyl-carrier protein] + AMP + diphosphate

Reactions known to produce the compound:

citrate lyase activation :
an acetyl-[holo citrate lyase acyl-carrier protein] + 6 H2O → [a holo citrate lyase acyl-carrier protein] + 6 acetate
2'-(5''-triphospho-α-D-ribosyl)-3'-dephospho-CoA + [an apo citrate-lyase acyl-carrier protein] → [a holo citrate lyase acyl-carrier protein] + diphosphate

Gene-Reaction Schematic: ?

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Subunit of citrate lyase, inactive: citrate lyase [acyl carrier protein] component

Synonyms: ybdX, CitD acyl carrier protein

Gene: citD Accession Numbers: G6343 (MetaCyc), b0617, ECK0610

Locations: cytosol

Subunit composition of citrate lyase [acyl carrier protein] component = [CitD]6
         citrate lyase, acyl carrier γ subunit = CitD

Map Position: [649,710 <- 650,006]

Molecular Weight of Polypeptide: 10.689 kD (from nucleotide sequence)

GO Terms:

Molecular Function: GO:0051192 - prosthetic group binding Inferred from experiment [Nilekani83]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents) large molecule carriers acyl carrier protein
metabolism central intermediary metabolism unassigned reversible reactions

Unification Links: EcoliWiki:b0617 , PR:PRO_000022289 , Protein Model Portal:P69330 , RefSeq:NP_415150 , String:511145.b0617 , UniProt:P69330

Relationship Links: InterPro:IN-FAMILY:IPR006495 , InterPro:IN-FAMILY:IPR023439 , Pfam:IN-FAMILY:PF06857 , ProDom:IN-FAMILY:PD015389

Reactions known to consume the compound:

citrate lyase activation :
[a holo citrate lyase acyl-carrier protein] + S-acetyl phosphopantetheine → an acetyl-[holo citrate lyase acyl-carrier protein] + 4'-phosphopantetheine
[a holo citrate lyase acyl-carrier protein] + acetate + ATP → an acetyl-[holo citrate lyase acyl-carrier protein] + AMP + diphosphate

Reactions known to produce the compound:

citrate lyase activation :
an acetyl-[holo citrate lyase acyl-carrier protein] + 6 H2O → [a holo citrate lyase acyl-carrier protein] + 6 acetate
2'-(5''-triphospho-α-D-ribosyl)-3'-dephospho-CoA + [an apo citrate-lyase acyl-carrier protein] → [a holo citrate lyase acyl-carrier protein] + diphosphate

Summary:
This component of the citrate lyase is made of 6 copies of the γ subunit, a specialized acyl carrier protein (acp). In the original purification of the enzyme, this subunit was purified with a contaminant and the complex structure was thought to be α-6 β-6 γ-1 [Nilekani83]. Subsequent work identified the contaminant, and the structure was recognized as α-6 β-6 γ-6 [Quentmeier87].

The [acp] subunit is activated by the covalent binding of an unusual prosthetic group, 2'-(5''-phosphoribosyl)-3'-dephospho-CoA, which is synthesized from the precursor 2'-(5''-triphospho-α-D-ribosyl)-3'-dephospho-CoA [Schneider00, Schneider00a] (see citrate lyase activation).


Subunit of citrate lyase, inactive: citrate lyase, citrate-ACP transferase component

Synonyms: ybdV

Gene: citF Accession Numbers: G6341 (MetaCyc), b0615, ECK0608

Locations: cytosol

Subunit composition of citrate lyase, citrate-ACP transferase component = [CitF]6
         citrate lyase, citrate-ACP transferase α subunit = CitF

Map Position: [647,262 <- 648,794]

Molecular Weight of Polypeptide: 55.173 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006084 - acetyl-CoA metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0008814 - citrate CoA-transferase activity Inferred by computational analysis [GOA01, GOA01a]
GO:0008815 - citrate (pro-3S)-lyase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0009346 - citrate lyase complex Inferred by computational analysis [GOA01a]

MultiFun Terms: metabolism central intermediary metabolism unassigned reversible reactions

Unification Links: EcoliWiki:b0615 , ModBase:P75726 , Pride:P75726 , Protein Model Portal:P75726 , RefSeq:NP_415148 , SMR:P75726 , String:511145.b0615 , Swiss-Model:P75726 , UniProt:P75726

Relationship Links: InterPro:IN-FAMILY:IPR006472 , Pfam:IN-FAMILY:PF04223


Subunit of citrate lyase, inactive: citrate lyase, citryl-ACP lyase component

Synonyms: ybdW

Gene: citE Accession Numbers: G6342 (MetaCyc), b0616, ECK0609

Locations: cytosol

Subunit composition of citrate lyase, citryl-ACP lyase component = [CitE]6
         citrate lyase, citryl-ACP lyase β subunit = CitE

Map Position: [648,805 <- 649,713]

Molecular Weight of Polypeptide: 33.11 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006084 - acetyl-CoA metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0008815 - citrate (pro-3S)-lyase activity Inferred by computational analysis [GOA01]
GO:0008816 - citryl-CoA lyase activity Inferred by computational analysis [GOA01, GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0009346 - citrate lyase complex Inferred by computational analysis [GOA01a]

MultiFun Terms: metabolism central intermediary metabolism unassigned reversible reactions

Unification Links: EcoliWiki:b0616 , Mint:MINT-1283346 , ModBase:P0A9I1 , PR:PRO_000022290 , Pride:P0A9I1 , Protein Model Portal:P0A9I1 , RefSeq:NP_415149 , SMR:P0A9I1 , String:511145.b0616 , UniProt:P0A9I1

Relationship Links: InterPro:IN-FAMILY:IPR005000 , InterPro:IN-FAMILY:IPR006475 , InterPro:IN-FAMILY:IPR011206 , InterPro:IN-FAMILY:IPR015813 , Pfam:IN-FAMILY:PF03328


References

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

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."

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

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

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."


Report Errors or Provide Feedback
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 18.5 on Sun Nov 23, 2014, BIOCYC14B.