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MetaCyc Protein: citrate lyase [acyl carrier protein] component

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

Synonyms: ybdX, CitD acyl carrier protein

Species: Escherichia coli K-12 substr. MG1655

Component of: citrate lyase, inactive

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

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

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).

Locations: cytosol

Map Position: [650,487 <- 650,783]

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

Unification Links: ASAP:ABE-0002124, EchoBASE:EB3313, EcoGene:EG13543, EcoliWiki:b0617, OU-Microarray:b0617, PortEco:citD, PR:PRO_000022289, Protein Model Portal:P69330, RefSeq:NP_415150, RegulonDB:G6343, 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] + acetate + ATP → an acetyl-[holo citrate lyase acyl-carrier protein] + AMP + diphosphate
[a holo citrate lyase acyl-carrier protein] + S-acetyl phosphopantetheine → an acetyl-[holo citrate lyase acyl-carrier protein] + 4'-phosphopantetheine

Reactions known to produce the compound:

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

Gene-Reaction Schematic

Gene-Reaction Schematic


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

MultiFun Terms: metabolismbiosynthesis of macromolecules (cellular constituents)large molecule carriersacyl carrier protein
metabolismcentral intermediary metabolismunassigned reversible reactions

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Subunit of: 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

Reactions known to consume the compound:

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

Reactions known to produce the compound:

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

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Sequence Features

Feature Class Location Citations Comment
Pfam PF06857 5 -> 86
Inferred by computational analysis[Finn14]
ACP : Malonate decarboxylase delta subunit (MdcD) [More...]
O-phosphoribosyl-CoA-Ser-Modification 14
Inferred by computational analysis[UniProt15]
UniProt: O-(phosphoribosyl dephospho-coenzyme A)serine.
Sequence-Conflict 93 -> 98
Inferred by curator[Oshima96, UniProt15]
UniProt: (in Ref. 2).

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

Oshima96: Oshima T, Aiba H, Baba T, Fujita K, Hayashi K, Honjo A, Ikemoto K, Inada T, Itoh T, Kajihara M, Kanai K, Kashimoto K, Kimura S, Kitagawa M, Makino K, Masuda S, Miki T, Mizobuchi K, Mori H, Motomura K, Nakamura Y, Nashimoto H, Nishio Y, Saito N, Horiuchi T (1996). "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." DNA Res 3(3);137-55. PMID: 8905232

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

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 Pathway Tools version 20.0 (software by SRI International) on Fri May 6, 2016, BIOCYC13.