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MetaCyc Enzyme: bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase

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

Synonyms: yacJ, yacI

Species: Escherichia coli K-12 substr. MG1655

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]

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

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

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

MultiFun Terms: metabolism carbon utilization carbon compounds
metabolism energy metabolism, carbon TCA cycle

Credits:
Created in EcoCyc 23-Feb-2009 by Keseler I , SRI International
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International


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

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

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

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

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)

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

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

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

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)

EC Number: 4.2.1.99

(2R,3S)-2-methylisocitrate <=> cis-2-methylaconitate + 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. [Brock02]

In Pathways: 2-methylcitrate cycle I

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

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

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 191
[UniProt15]
UniProt: Substrate.
Protein-Segment 244 -> 246
[UniProt10b]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Protein-Segment 414 -> 416
[UniProt10b]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 498
[UniProt15]
UniProt: Substrate.
Acetylation-Modification 559
[Yu08]
 
Metal-Binding-Site 710
[Williams02, UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 769
[Williams02, UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 772
[Williams02, UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Amino-Acid-Sites-That-Bind 791
[UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 796
[UniProt15]
UniProt: Substrate.

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


References

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

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

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

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

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-12 released on 2010-12-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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

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


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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