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Escherichia coli K-12 substr. MG1655 Enzyme: citrate synthase

Gene: gltA Accession Numbers: EG10402 (EcoCyc), b0720, ECK0709

Synonyms: glut, icdB

Regulation Summary Diagram: ?

Subunit composition of citrate synthase = [GltA]6
         citrate synthase monomer = GltA

The E. coli citrate synthase is a type II enzyme, which appears to be unique to the Gram-negative bacteria. It behaves like a trimer of dimeric subunits; the dimer is the basic catalytic unit, but the hexameric form is required for allosteric inhibition by NADH. By contrast, citrate synthase from animals, plants and some bacteria is a simple dimer that is not allosterically regulated. [Else88]

Enzyme synthesis is subject to catabolite repression, is repressed by glucose and anaerobiosis, and induced by acetate and oxygen. When acetate is the carbon source, citrate synthase is rate-limiting for the TCA cycle. [Walsh85a, Walsh87]

Crystal structures of citrate synthase have been solved, providing insight into the allosteric regulatory mechanism of the enzyme [Nguyen01, Maurus03, Stokell03].

Gene Citations: [Wilde86, Cunningham98a]

Locations: cytosol

Map Position: [752,408 <- 753,691] (16.22 centisomes)
Length: 1284 bp / 427 aa

Molecular Weight of Polypeptide: 48.015 kD (from nucleotide sequence)

pI: 6.62

Unification Links: ASAP:ABE-0002451 , CGSC:687 , DIP:DIP-36204N , EchoBASE:EB0397 , EcoGene:EG10402 , EcoliWiki:b0720 , Mint:MINT-1249502 , ModBase:P0ABH7 , OU-Microarray:b0720 , PortEco:gltA , PR:PRO_000022803 , Pride:P0ABH7 , Protein Model Portal:P0ABH7 , RefSeq:NP_415248 , RegulonDB:EG10402 , SMR:P0ABH7 , String:511145.b0720 , UniProt:P0ABH7

Relationship Links: InterPro:IN-FAMILY:IPR002020 , InterPro:IN-FAMILY:IPR010953 , InterPro:IN-FAMILY:IPR016141 , InterPro:IN-FAMILY:IPR016142 , InterPro:IN-FAMILY:IPR016143 , InterPro:IN-FAMILY:IPR019810 , InterPro:IN-FAMILY:IPR024176 , Panther:IN-FAMILY:PTHR11739 , PDB:Structure:1K3P , PDB:Structure:1NXE , PDB:Structure:1NXG , PDB:Structure:1OWB , PDB:Structure:1OWC , PDB:Structure:3L96 , PDB:Structure:3L97 , PDB:Structure:3L98 , PDB:Structure:3L99 , PDB:Structure:4JAD , PDB:Structure:4JAE , PDB:Structure:4JAF , PDB:Structure:4JAG , Pfam:IN-FAMILY:PF00285 , Prints:IN-FAMILY:PR00143 , Prosite:IN-FAMILY:PS00480

In Paralogous Gene Group: 184 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006099 - tricarboxylic acid cycle Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0044262 - cellular carbohydrate metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Lasserre06]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11]
GO:0004108 - citrate (Si)-synthase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0046912 - transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [GOA01]

MultiFun Terms: metabolism energy metabolism, carbon TCA cycle

Essentiality data for gltA 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 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 4]

Enzymatic reaction of: citrate synthase

Synonyms: condensing enzyme, citrogenase, oxalaoacetate transacetylase

EC Number:

oxaloacetate + acetyl-CoA + H2O <=> citrate + coenzyme A + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass , superpathway of glyoxylate bypass and TCA , glyoxylate cycle , TCA cycle I (prokaryotic) , mixed acid fermentation

Citations: [Duckworth87, Anderson88b, Walsh85a]

Activators (Allosteric): acetyl-CoA

Activators (Non-Allosteric): K+

Inhibitors (Allosteric): NAD+ , oxaloacetate , NADH

Inhibitors (Competitive): ATP , 2-oxoglutarate

Inhibitors (Unknown Mechanism): propanoyl-CoA [Man95] , carboxymethyl-CoA [Man95]

Primary Physiological Regulators of Enzyme Activity: NADH , 2-oxoglutarate

Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 11
[Bhayana84, UniProt10]
Alternate sequence: N → D; UniProt: (in Ref. 6; AA sequence);
Mutagenesis-Variant 207
[Donald91, UniProt11]
Alternate sequence: C → S; UniProt: Weakened NADH binding and inhibition.
Mutagenesis-Variant 208
[Donald91, UniProt11]
Alternate sequence: E → A; UniProt: Weakened NADH binding and inhibition.
Acetylation-Modification 283
[Zhang, 2009, UniProt11]
UniProt: N6-acetyllysine.
Sequence-Conflict 289
[Ner83, Bhayana84, UniProt10]
Alternate sequence: V → F; UniProt: (in Ref. 1; AAA23892 and 6; AA sequence);
Active-Site 306
UniProt: Non-Experimental Qualifier: by similarity;
Acetylation-Modification 356
Active-Site 363
UniProt: Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Transcription Units:


10/20/97 Gene b0720 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10402; confirmed by SwissProt match.


Anderson88b: Anderson DH, Duckworth HW (1988). "In vitro mutagenesis of Escherichia coli citrate synthase to clarify the locations of ligand binding sites." J Biol Chem 1988;263(5);2163-9. PMID: 3276685

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

Bhayana84: Bhayana V, Duckworth HW (1984). "Amino acid sequence of Escherichia coli citrate synthase." Biochemistry 23(13);2900-5. PMID: 6380576

Cunningham98a: Cunningham L, Guest JR (1998). "Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli." Microbiology 144 ( Pt 8);2113-23. PMID: 9720032

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

Donald91: Donald LJ, Crane BR, Anderson DH, Duckworth HW (1991). "The role of cysteine 206 in allosteric inhibition of Escherichia coli citrate synthase. Studies by chemical modification, site-directed mutagenesis, and 19F NMR." J Biol Chem 266(31);20709-13. PMID: 1939121

Duckworth87: Duckworth HW, Anderson DH, Bell AW, Donald LJ, Chu AL, Brayer GD (1987). "Structural basis for regulation in gram-negative bacterial citrate synthases." Biochem Soc Symp 1987;54;83-92. PMID: 3333000

Else88: Else AJ, Danson MJ, Weitzman PD (1988). "Models of proteolysis of oligomeric enzymes and their applications to the trypsinolysis of citrate synthases." Biochem J 1988;254(2);437-42. PMID: 3140803

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."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Man95: Man WJ, Li Y, O'Connor CD, Wilton DC (1995). "The binding of propionyl-CoA and carboxymethyl-CoA to Escherichia coli citrate synthase." Biochim Biophys Acta 1250(1);69-75. PMID: 7612655

Maurus03: Maurus R, Nguyen NT, Stokell DJ, Ayed A, Hultin PG, Duckworth HW, Brayer GD (2003). "Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases." Biochemistry 42(19);5555-65. PMID: 12741811

Ner83: Ner S.S., Bhayana V., Bell A.W., Giles I.G., Duckworth H.W., Bloxham D.P. (1983). "Complete sequence of the gltA gene encoding citrate synthase in Escherichia coli." Biochemistry, Volume 22, page(s) 5243-5249.

Nguyen01: Nguyen NT, Maurus R, Stokell DJ, Ayed A, Duckworth HW, Brayer GD (2001). "Comparative analysis of folding and substrate binding sites between regulated hexameric type II citrate synthases and unregulated dimeric type I enzymes." Biochemistry 40(44);13177-87. PMID: 11683626

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Stokell03: Stokell DJ, Donald LJ, Maurus R, Nguyen NT, Sadler G, Choudhary K, Hultin PG, Brayer GD, Duckworth HW (2003). "Probing the roles of key residues in the unique regulatory NADH binding site of type II citrate synthase of Escherichia coli." J Biol Chem 278(37);35435-43. PMID: 12824188

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Walsh85a: Walsh K, Koshland DE (1985). "Characterization of rate-controlling steps in vivo by use of an adjustable expression vector." Proc Natl Acad Sci U S A 1985;82(11);3577-81. PMID: 3889909

Walsh87: Walsh K, Schena M, Flint AJ, Koshland DE (1987). "Compensatory regulation in metabolic pathways--responses to increases and decreases in citrate synthase levels." Biochem Soc Symp 1987;54;183-95. PMID: 3332995

Wilde86: Wilde RJ, Guest JR (1986). "Transcript analysis of the citrate synthase and succinate dehydrogenase genes of Escherichia coli K12." J Gen Microbiol 1986;132 ( Pt 12);3239-51. PMID: 3309132

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Zhang, 2009: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Beisel11: Beisel CL, Storz G (2011). "The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli." Mol Cell 41(3);286-97. PMID: 21292161

Iuchi90a: Iuchi S, Matsuda Z, Fujiwara T, Lin EC (1990). "The arcB gene of Escherichia coli encodes a sensor-regulator protein for anaerobic repression of the arc modulon." Mol Microbiol 1990;4(5);715-27. PMID: 2201868

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Lynch96: Lynch AS, Lin EC (1996). "Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters." J Bacteriol 1996;178(21);6238-49. PMID: 8892825

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Park94: Park SJ, McCabe J, Turna J, Gunsalus RP (1994). "Regulation of the citrate synthase (gltA) gene of Escherichia coli in response to anaerobiosis and carbon supply: role of the arcA gene product." J Bacteriol 1994;176(16);5086-92. PMID: 8051021

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

ShalelLevanon05a: Shalel-Levanon S, San KY, Bennett GN (2005). "Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli." Metab Eng 7(5-6):364-74. PMID: 16140031

Wood84: Wood D, Darlison MG, Wilde RJ, Guest JR (1984). "Nucleotide sequence encoding the flavoprotein and hydrophobic subunits of the succinate dehydrogenase of Escherichia coli." Biochem J 1984;222(2);519-34. PMID: 6383359

Zhang05: Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, Saier MH (2005). "Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli." J Bacteriol 187(3);980-90. PMID: 15659676

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470

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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 Sat Nov 22, 2014, BIOCYC14A.