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Escherichia coli K-12 substr. MG1655 Enzyme: bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase




Gene: acnB Accession Numbers: EG12316 (EcoCyc), b0118, ECK0117

Synonyms: yacJ, yacI

Regulation Summary Diagram

Regulation summary diagram for acnB

Subunit composition of bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase = [AcnB]2
         bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase = AcnB

Summary:
There are two aconitases in E. coli, both of which catalyze the reversible isomerization of citrate and iso-citrate via cis-aconitate. AcnB also plays a role in the methylcitrate cycle for degradation of propionate, where it is responsible for hydration of 2-methyl-cis-aconitate to (2R,3S)-2-methylisocitrate [Brock02]. The apo form of AcnB is able to bind mRNA and enhances translation of AcnB [Tang99].

AcnB appears to function as the main catabolic enzyme, while the main role of AcnA appears to be as a maintenance or survival enzyme during nutritional or oxidative stress [Cunningham97]. The AcnB enzyme is less stable, has a lower affinity for citrate and is active over a more narrow pH range than the AcnA enzyme [Jordan99, Varghese03]. Unlike AcnA, AcnB is sensitive to oxidation in vivo [Brock02, Varghese03]. AcnB rapidly loses catalytic activity when the iron concentration is low [Varghese03].

The N-terminal region of AcnB mediates the formation of AcnB homodimers in the presence of Fe2+; the 4Fe-4S cluster or catalytic activity is not required for dimer formation. In the absence of Fe2+, the same region is able to bind to mRNA [Tang05]. AcnB also interacts weakly with isocitrate dehydrogenase [Tsuchiya08]. The catalytically inactive AcnB apo-protein, lacking its iron-sulfur cluster, has a negative effect on SodA synthesis in vitro [Tang02].

IscA or SufA are required for assembly of the [4Fe-4S] cluster in AcnB [Tan09].

A crystal structure of AcnB has been solved at 2.4 Å resolution [Williams02].

An acnB mutant does not grow on acetate as the sole source of carbon, grows poorly on other carbon sources such as glucose and pyruvate [Gruer97], contains high levels of citrate, and excretes substantial amounts of citrate into the medium [Varghese03]. An acnB mutant is more sensitive to peroxide stress than wild type and shows increased SodA synthesis [Tang02].

Expression of acnB increases early in exponential phase and decreases during entry into stationary phase [Gruer97, Cunningham97].

Reviews: [Gruer97a, Kiley03]

Citations: [Calderon09, Stefanopoulou11, Maci12]

Locations: cytosol

Map Position: [131,615 -> 134,212] (2.84 centisomes, 10°)
Length: 2598 bp / 865 aa

Molecular Weight of Polypeptide: 93.498 kD (from nucleotide sequence), 94 kD (experimental) [Brock02]

Molecular Weight of Multimer: 180.0 kD (experimental) [Tang05]

Unification Links: ASAP:ABE-0000411, CGSC:36955, DIP:DIP-9044N, EchoBASE:EB2222, EcoGene:EG12316, EcoliWiki:b0118, ModBase:P36683, OU-Microarray:b0118, PortEco:acnB, PR:PRO_000022043, Pride:P36683, Protein Model Portal:P36683, RefSeq:NP_414660, RegulonDB:EG12316, SMR:P36683, String:511145.b0118, UniProt:P36683

Relationship Links: InterPro:IN-FAMILY:IPR001030, InterPro:IN-FAMILY:IPR004406, InterPro:IN-FAMILY:IPR015928, InterPro:IN-FAMILY:IPR015929, InterPro:IN-FAMILY:IPR015931, InterPro:IN-FAMILY:IPR015932, InterPro:IN-FAMILY:IPR015933, InterPro:IN-FAMILY:IPR015937, InterPro:IN-FAMILY:IPR018136, Panther:IN-FAMILY:PTHR11670, PDB:Structure:1L5J, Pfam:IN-FAMILY:PF00330, Pfam:IN-FAMILY:PF06434, Pfam:IN-FAMILY:PF11791, 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 acnB


GO Terms:
Biological Process:
Inferred from experimentGO:0006417 - regulation of translation [Tang99]
Inferred from experimentGO:0019629 - propionate catabolic process, 2-methylcitrate cycle [Brock02]
Author statementGO:0006097 - glyoxylate cycle [Tang99]
Author statementInferred by computational analysisGO:0006099 - tricarboxylic acid cycle [UniProtGOA12, UniProtGOA11a, GOA01a, Tang99]
Inferred by computational analysisGO:0008152 - metabolic process [GOA01a]
Molecular Function:
Inferred from experimentGO:0003729 - mRNA binding [Tang99, Tang05]
Inferred from experimentGO:0003730 - mRNA 3'-UTR binding [Tang99]
Inferred from experimentInferred by computational analysisGO:0003994 - aconitate hydratase activity [GOA01, GOA01a, Jordan99, Bradbury96]
Inferred from experimentGO:0005515 - protein binding [Kumar04]
Inferred from experimentInferred by computational analysisGO:0047456 - 2-methylisocitrate dehydratase activity [GOA01, Brock02]
Inferred from experimentInferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a, GOA01a, Jordan99]
Inferred by computational analysisGO:0003723 - RNA binding [UniProtGOA11a]
Inferred by computational analysisGO:0016829 - lyase activity [UniProtGOA11a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [GOA01a, DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolismcarbon utilizationcarbon compounds
metabolismenergy metabolism, carbonTCA cycle

Essentiality data for acnB knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Created 23-Feb-2009 by Keseler I, SRI International
Last-Curated 02-Aug-2012 by Keseler I, SRI International


Enzymatic reaction of: D-threo-isocitrate hydro-lyase (bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase)

Inferred from experiment

Synonyms: aconitase B, isocitrate hydro-lyase, aconitate hydratase

cis-aconitate + H2O ⇄ D-threo-isocitrate

The direction shown, i.e. which substrates are on the left and right sides, 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), mixed acid fermentation

Summary:
The enzyme shows weak negative cooperativity for isomerization of isocitrate, with a Hill coefficient of 0.727 [Tsuchiya09].

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Gruer94, Jordan99]

Kinetic Parameters:
Substrate Km (μM) Citations
cis-aconitate 16.0 [Jordan99]
D-threo-isocitrate 51.0 [Jordan99]

pH(opt): 7.4 [Jordan99]


Enzymatic reaction of: citrate hydro-lyase (bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase)

Inferred from experiment

Synonyms: aconitase B, citrate hydro-lyase, aconitate hydratase

citrate ⇄ cis-aconitate + H2O

The direction shown, i.e. which substrates are on the left and right sides, 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), mixed acid fermentation

Summary:
The enzyme shows weak positive cooperativity for isomerization of citrate, with a Hill coefficient of 1.229 [Tsuchiya09].

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Gruer94, Jordan99]

Kinetic Parameters:
Substrate Km (μM) Citations
cis-aconitate 16.0 [Jordan99]
citrate 11000.0 [Jordan99]

pH(opt): 7.4 [Jordan99]


Enzymatic reaction of: (2R,3S)-2-methylisocitrate hydro-lyase (bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase)

Inferred from experiment

EC Number: 4.2.1.99

(2R,3S)-2-methylisocitrate ⇄ cis-2-methylaconitate + H2O

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Brock02]

In Pathways: 2-methylcitrate cycle I

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Brock02]

Kinetic Parameters:
Substrate Km (μM) Citations
(2R,3S)-2-methylisocitrate 210.0 [Brock02]

Sequence Features

Protein sequence of bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase with features indicated

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 191
Inferred from experiment[Williams02]
UniProt: Substrate.
Protein-Segment 244 -> 246
Inferred from experiment[Williams02]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Protein-Segment 414 -> 416
Inferred from experiment[Williams02]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 498
Inferred from experiment[Williams02]
UniProt: Substrate.
Acetylation-Modification 559
Inferred from experiment[Yu08]
 
Metal-Binding-Site 710
Inferred from experiment[Williams02]
UniProt: Iron-sulfur (4Fe-4S).
Mutagenesis-Variant 769
Inferred from experiment[Tang05]
UniProt: Inhibits the dimer formation.
Metal-Binding-Site 769
Inferred from experiment[Williams02]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 772
Inferred from experiment[Williams02]
UniProt: Iron-sulfur (4Fe-4S).
Amino-Acid-Sites-That-Bind 791
Inferred from experiment[Williams02]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 796
Inferred from experiment[Williams02]
UniProt: Substrate.


Sequence Pfam Features

Protein sequence of bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase with features indicated

Feature Class Location Citations Comment
Pfam PF11791 4 -> 156
Inferred by computational analysis[Finn14]
Aconitase_B_N : Aconitate B N-terminal domain
Pfam PF06434 168 -> 382
Inferred by computational analysis[Finn14]
Aconitase_2_N : Aconitate hydratase 2 N-terminus
Pfam PF00330 470 -> 818
Inferred by computational analysis[Finn14]
Aconitase : Aconitase family (aconitate hydratase)


Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b0118 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12316; confirmed by SwissProt match.


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

Bradbury96: Bradbury AJ, Gruer MJ, Rudd KE, Guest JR (1996). "The second aconitase (AcnB) of Escherichia coli." Microbiology 142 ( Pt 2);389-400. PMID: 8932712

Brock02: Brock M, Maerker C, Schutz A, Volker U, Buckel W (2002). "Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase." Eur J Biochem 269(24);6184-94. PMID: 12473114

Calderon09: Calderon IL, Elias AO, Fuentes EL, Pradenas GA, Castro ME, Arenas FA, Perez JM, Vasquez CC (2009). "Tellurite-mediated disabling of [4Fe-4S] clusters of Escherichia coli dehydratases." Microbiology 155(Pt 6);1840-6. PMID: 19383690

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

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

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

Gruer97: Gruer MJ, Bradbury AJ, Guest JR (1997). "Construction and properties of aconitase mutants of Escherichia coli." Microbiology 143 ( Pt 6);1837-46. PMID: 9202458

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

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

Kumar04: Kumar JK, Tabor S, Richardson CC (2004). "Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli." Proc Natl Acad Sci U S A 101(11);3759-64. PMID: 15004283

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

Maci12: Maciąg M, Nowicki D, Szalewska-Palasz A, Węgrzyn G (2012). "Central carbon metabolism influences fidelity of DNA replication in Escherichia coli." Mutat Res 731(1-2);99-106. PMID: 22198407

Park06: Park YJ, Yoo CB, Choi SY, Lee HB (2006). "Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1." J Biochem Mol Biol 39(1);46-54. PMID: 16466637

Stefanopoulou11: Stefanopoulou M, Kokoschka M, Sheldrick WS, Wolters DA (2011). "Cell response of Escherichia coli to cisplatin-induced stress." Proteomics 11(21);4174-88. PMID: 21972224

Tan09: Tan G, Lu J, Bitoun JP, Huang H, Ding H (2009). "IscA/SufA paralogues are required for the [4Fe-4S] cluster assembly in enzymes of multiple physiological pathways in Escherichia coli under aerobic growth conditions." Biochem J 420(3);463-72. PMID: 19309314

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

Tang05: Tang Y, Guest JR, Artymiuk PJ, Green J (2005). "Switching aconitase B between catalytic and regulatory modes involves iron-dependent dimer formation." Mol Microbiol 56(5);1149-58. PMID: 15882410

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

Tsuchiya08: Tsuchiya D, Shimizu N, Tomita M (2008). "Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase." Biochim Biophys Acta 1784(11);1847-56. PMID: 18640291

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

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

Williams02: Williams CH, Stillman TJ, Barynin VV, Sedelnikova SE, Tang Y, Green J, Guest JR, Artymiuk PJ (2002). "E. coli aconitase B structure reveals a HEAT-like domain with implications for protein-protein recognition." Nat Struct Biol 9(6);447-52. PMID: 11992126

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

Other References Related to Gene Regulation

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

Trotter11: Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP, Sanguinetti G, Poole RK, Green J (2011). "Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment." PLoS One 6(9);e25501. PMID: 21980479


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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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