Escherichia coli K-12 substr. MG1655 Enzyme: aconitate hydratase 1

Gene: acnA Accession Numbers: EG11325 (EcoCyc), b1276, ECK1271

Synonyms: acn, aconitase, isocitrate hydro-lyase

Regulation Summary Diagram: ?

Regulation summary diagram for acnA

Subunit composition of aconitate hydratase 1 = [AcnA]2
         aconitate hydratase 1 = AcnA

There are two aconitases in E. coli, both of which catalyze the reversible isomerization of citrate and iso-citrate via cis-aconitate. The apo form of AcnA is able to bind mRNA and enhances translation of AcnA [Tang99].

The AcnA enzyme is more stable, has a higher affinity for citrate and is active over a wider pH range than the AcnB enzyme [Jordan99, Varghese03]. Unlike AcnB, AcnA is resistant to oxidation in vivo [Varghese03]. The main role of the AcnA enzyme appears to be as a maintenance or survival enzyme during nutritional or oxidative stress, while the AcnB enzyme appears to function as the main catabolic enzyme [Cunningham97].

The catalytically inactive AcnA apo-protein, lacking its iron-sulfur cluster, is able to bind mRNA and enhances translation of AcnA [Tang99] and has a positive effect on SodA synthesis [Tang02].

Cells grown in the presence of nitrate contain lower levels of aconitase and fumarase [Prodromou91]. Synthesis of AcnA is subject to catabolite and anaerobic repression [Gruer94] and is induced by salt stress under aerobic conditions [Weber06]. acnA expression is induced under oxidative stress [Lu04, Lu05]. Expression of AcnA is posttranscriptionally downregulated in response to low iron levels by the small RNA RyhB [Masse02].

An acnA mutant is more susceptible to pyrazinoic acid than wild type [Schaller02].

Reviews: [Gruer97a, Kiley03]

Citations: [Prodromou92]

Locations: cytosol

Map Position: [1,333,855 -> 1,336,530] (28.75 centisomes, 103°)
Length: 2676 bp / 891 aa

Molecular Weight of Polypeptide: 97.677 kD (from nucleotide sequence)

Molecular Weight of Multimer: 193.0 kD (experimental) [Tsuchiya09]

Unification Links: ASAP:ABE-0004283 , CGSC:28218 , DIP:DIP-9043N , EchoBASE:EB1301 , EcoGene:EG11325 , EcoliWiki:b1276 , Mint:MINT-1249275 , ModBase:P25516 , OU-Microarray:b1276 , PortEco:acnA , PR:PRO_000022042 , Pride:P25516 , Protein Model Portal:P25516 , RefSeq:NP_415792 , RegulonDB:EG11325 , SMR:P25516 , String:511145.b1276 , UniProt:P25516

Relationship Links: InterPro:IN-FAMILY:IPR000573 , InterPro:IN-FAMILY:IPR001030 , InterPro:IN-FAMILY:IPR006249 , InterPro:IN-FAMILY:IPR015928 , InterPro:IN-FAMILY:IPR015931 , InterPro:IN-FAMILY:IPR015932 , InterPro:IN-FAMILY:IPR015934 , InterPro:IN-FAMILY:IPR015937 , InterPro:IN-FAMILY:IPR018136 , Panther:IN-FAMILY:PTHR11670 , Panther:IN-FAMILY:PTHR11670:SF1 , Pfam:IN-FAMILY:PF00330 , Pfam:IN-FAMILY:PF00694 , Prints:IN-FAMILY:PR00415 , Prosite:IN-FAMILY:PS00450 , Prosite:IN-FAMILY:PS01244

In Paralogous Gene Group: 27 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for acnA

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Varghese03]
GO:0009061 - anaerobic respiration Inferred from experiment [Varghese03]
GO:0006097 - glyoxylate cycle Author statement [Tang99]
GO:0006099 - tricarboxylic acid cycle Author statement Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, Tang99]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003729 - mRNA binding Inferred from experiment [Tang99]
GO:0003730 - mRNA 3'-UTR binding Inferred from experiment [Tang99]
GO:0003994 - aconitate hydratase activity Inferred from experiment Inferred by computational analysis [GOA01, Bennett95, Prodromou91]
GO:0005506 - iron ion binding Inferred from experiment [Varghese03]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Varghese03]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Varghese03, Bennett95]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Varghese03]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: cell processes adaptations other (mechanical, nutritional, oxidative stress)
metabolism energy metabolism, carbon TCA cycle
regulation type of regulation posttranscriptional

Essentiality data for acnA 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]

Created 23-Feb-2009 by Keseler I , SRI International
Last-Curated ? 26-Feb-2009 by Keseler I , SRI International

Enzymatic reaction of: D-threo-isocitrate hydro-lyase (cis-aconitate-forming) (aconitate hydratase 1)

cis-aconitate + H2O <=> D-threo-isocitrate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

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

The enzyme shows negative cooperativity for isomerization of isocitrate, with a Hill coefficient of 0.718 [Tsuchiya09].

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Bennett95, Jordan99]

Kinetic Parameters:

Km (μM)

pH(opt): 7.4 [Jordan99]

Enzymatic reaction of: citrate hydro-lyase (cis-aconitate-forming) (aconitate hydratase 1)

citrate <=> cis-aconitate + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

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

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Bennett95, Jordan99]

Kinetic Parameters:

Km (μM)

pH(opt): 7.4 [Jordan99]

Sequence Features

Protein sequence of aconitate hydratase 1 with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Prodromou91, UniProt11]
UniProt: Removed.
Chain 2 -> 891
UniProt: Aconitate hydratase 1;
Metal-Binding-Site 435
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 501
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 504
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Sequence-Conflict 522
[Prodromou92, Hayashi06a, UniProt10a]
UniProt: (in Ref. 1; CAA42834 and 4; BAA14828);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1276 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11325; confirmed by SwissProt match.


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

Bennett95: Bennett B, Gruer MJ, Guest JR, Thomson AJ (1995). "Spectroscopic characterisation of an aconitase (AcnA) of Escherichia coli." Eur J Biochem 233(1);317-26. PMID: 7588761

Cunningham97: Cunningham L, Gruer MJ, Guest JR (1997). "Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli." Microbiology 143 ( Pt 12);3795-805. PMID: 9421904

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, 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."

Gruer94: Gruer MJ, Guest JR (1994). "Two genetically-distinct and differentially-regulated aconitases (AcnA and AcnB) in Escherichia coli." Microbiology 1994;140 ( Pt 10);2531-41. PMID: 8000525

Gruer97a: Gruer MJ, Artymiuk PJ, Guest JR (1997). "The aconitase family: three structural variations on a common theme." Trends Biochem Sci 22(1);3-6. PMID: 9020582

Hayashi06a: Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2;2006.0007. PMID: 16738553

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

Jordan99: Jordan PA, Tang Y, Bradbury AJ, Thomson AJ, Guest JR (1999). "Biochemical and spectroscopic characterization of Escherichia coli aconitases (AcnA and AcnB)." Biochem J 1999;344 Pt 3;739-46. PMID: 10585860

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

Kiley03: Kiley PJ, Beinert H (2003). "The role of Fe-S proteins in sensing and regulation in bacteria." Curr Opin Microbiol 6(2);181-5. PMID: 12732309

Lu04: Lu C, Bentley WE, Rao G (2004). "A high-throughput approach to promoter study using green fluorescent protein." Biotechnol Prog 20(6);1634-40. PMID: 15575693

Lu05: Lu C, Albano CR, Bentley WE, Rao G (2005). "Quantitative and kinetic study of oxidative stress regulons using green fluorescent protein." Biotechnol Bioeng 89(5);574-87. PMID: 15672380

Masse02: Masse E, Gottesman S (2002). "A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli." Proc Natl Acad Sci U S A 99(7);4620-5. PMID: 11917098

Prodromou91: Prodromou C, Haynes MJ, Guest JR (1991). "The aconitase of Escherichia coli: purification of the enzyme and molecular cloning and map location of the gene (acn)." J Gen Microbiol 1991;137 ( Pt 11);2505-15. PMID: 1838390

Prodromou92: Prodromou C, Artymiuk PJ, Guest JR (1992). "The aconitase of Escherichia coli. Nucleotide sequence of the aconitase gene and amino acid sequence similarity with mitochondrial aconitases, the iron-responsive-element-binding protein and isopropylmalate isomerases." Eur J Biochem 1992;204(2);599-609. PMID: 1541275

Schaller02: Schaller A, Guo M, Gisanrin O, Zhang Y (2002). "Escherichia coli genes involved in resistance to pyrazinoic acid, the active component of the tuberculosis drug pyrazinamide." FEMS Microbiol Lett 211(2);265-70. PMID: 12076823

Tang02: Tang Y, Quail MA, Artymiuk PJ, Guest JR, Green J (2002). "Escherichia coli aconitases and oxidative stress: post-transcriptional regulation of sodA expression." Microbiology 148(Pt 4);1027-37. PMID: 11932448

Tang99: Tang Y, Guest JR (1999). "Direct evidence for mRNA binding and post-transcriptional regulation by Escherichia coli aconitases." Microbiology 145 ( Pt 11);3069-79. PMID: 10589714

Tsuchiya09: Tsuchiya D, Shimizu N, Tomita M (2009). "Cooperativity of two active sites in bacterial homodimeric aconitases." Biochem Biophys Res Commun 379(2);485-8. PMID: 19116142

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

UniProtGOA11a: 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."

Varghese03: Varghese S, Tang Y, Imlay JA (2003). "Contrasting sensitivities of Escherichia coli aconitases A and B to oxidation and iron depletion." J Bacteriol 185(1);221-30. PMID: 12486059

Weber06: Weber A, Kogl SA, Jung K (2006). "Time-dependent proteome alterations under osmotic stress during aerobic and anaerobic growth in Escherichia coli." J Bacteriol 188(20);7165-75. PMID: 17015655

Other References Related to Gene Regulation

Baez13: Baez A, Shiloach J (2013). "Escherichia coli avoids high dissolved oxygen stress by activation of SoxRS and manganese-superoxide dismutase." Microb Cell Fact 12;23. PMID: 23497217

Fuentes01: Fuentes AM, Diaz-Mejia JJ, Maldonado-Rodriguez R, Amabile-Cuevas CF (2001). "Differential activities of the SoxR protein of Escherichia coli: SoxS is not required for gene activation under iron deprivation." FEMS Microbiol Lett 201(2);271-5. PMID: 11470373

Lu03: Lu C, Bentley WE, Rao G (2003). "Comparisons of oxidative stress response genes in aerobic Escherichia coli fermentations." Biotechnol Bioeng 83(7);864-70. PMID: 12889026

Martin02: Martin RG, Rosner JL (2002). "Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data." Mol Microbiol 44(6);1611-24. PMID: 12067348

Martin11: Martin RG, Rosner JL (2011). "Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli." J Bacteriol 193(2);506-15. PMID: 21097628

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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