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Escherichia coli K-12 substr. MG1655 Protein: citrate lyase, inactive

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

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] + 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] + 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: ?


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

Synonyms: ybdX, CitD acyl carrier protein

Gene: citD Accession Numbers: G6343 (EcoCyc), 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] (14.0 centisomes)
Length: 297 bp / 98 aa

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 [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]
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] + 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] + 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).

Essentiality data for citD 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]

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

Synonyms: ybdV

Gene: citF Accession Numbers: G6341 (EcoCyc), 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] (13.95 centisomes)
Length: 1533 bp / 510 aa

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

GO Terms:

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

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

Essentiality data for citF 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]

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

Synonyms: ybdW

Gene: citE Accession Numbers: G6342 (EcoCyc), 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] (13.98 centisomes)
Length: 909 bp / 302 aa

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

GO Terms:

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

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

Essentiality data for citE 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]

References

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

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

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."

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

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 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."


Report Errors or Provide Feedback
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 18.5 on Fri Nov 28, 2014, biocyc14.