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Escherichia coli K-12 substr. MG1655 Enzyme: fumarase A



Gene: fumA Accession Numbers: EG10356 (EcoCyc), b1612, ECK1607

Regulation Summary Diagram: ?

Subunit composition of fumarase A = [FumA]2
         fumarase A monomer = FumA

Summary:
Fumarase A (FumA) is one of three fumarase isozymes participating in the TCA cycle. FumA is a dimeric [4Fe-4S] cluster-containing protein and belongs to the class I fumarases [Woods88, Flint92]. Fumarase A can also catalyze the isomerization of enol- to keto-oxalacetate [Flint93c].

The cell adapts to changing environmental oxygen conditions by utilizing different isozymes. Both FumA and FumB contain iron-sulfur centers; exposure to oxidative agents such as superoxide results in damage to the metal cofactor and loss of enzyme activity [Flint93b]. In contrast, FumC is an iron-independent enzyme and is insensitive to oxidative damage [Flint94]. FumC is made by the cells primarily as a backup enzyme if the FumA or FumB enzymes are damaged by reactive oxygen species. [Liochev93, Tseng01]

Expression of all three fumarase genes is anaerobically controlled. Expression of fumB is four fold elevated under anaerobic cell growth conditions versus aerobic conditions [Tseng97]. In contrast, fumA expression is highest only during aerobic growth and where fumC is only weakly expressed. When cells encounter oxidative stress conditions, fumC gene expression is then significantly induced by the SoxRS regulatory system [Park95a]. The aerobic/anaerobic transcriptional regulators ArcA and Fnr function to repress fumA as well as fumC gene expression under anaerobic conditions.

The complex regulation of fumA expression has been investigated [Woods87, Gruer94, Park95a, Lara06, Ojima08, Chen12a]. Regulation of fumA expression by Fur may be indirect, via the small RNA RyhB [Masse02, Prevost11]. Steady-state levels of fumA mRNA decrease with increasing growth rate; conversely, the half life of fumA mRNA increases, leading to unchanged levels of FumA protein [Lin12a].

Citations: [Calderon09, Gray66]

Gene Citations: [Miles84, Miles84a]

Locations: cytosol

Map Position: [1,684,755 <- 1,686,401] (36.31 centisomes)
Length: 1647 bp / 548 aa

Molecular Weight of Polypeptide: 60.299 kD (from nucleotide sequence), 61.5 kD (experimental) [Guest83 ]

Molecular Weight of Multimer: 120.0 kD (experimental) [Woods88]

Isozyme Sequence Similarity:
fumarase B monomer: YES

Unification Links: ASAP:ABE-0005392 , CGSC:18292 , DIP:DIP-36200N , EchoBASE:EB0351 , EcoGene:EG10356 , EcoliWiki:b1612 , Mint:MINT-1310290 , OU-Microarray:b1612 , PortEco:fumA , PR:PRO_000022734 , Pride:P0AC33 , Protein Model Portal:P0AC33 , RefSeq:NP_416129 , RegulonDB:EG10356 , SMR:P0AC33 , String:511145.b1612 , UniProt:P0AC33

Relationship Links: InterPro:IN-FAMILY:IPR004646 , InterPro:IN-FAMILY:IPR004647 , InterPro:IN-FAMILY:IPR011167 , InterPro:IN-FAMILY:IPR020557 , Pfam:IN-FAMILY:PF05681 , Pfam:IN-FAMILY:PF05683 , Prosite:IN-FAMILY:PS00163

In Paralogous Gene Group: 318 (3 members) , 484 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006099 - tricarboxylic acid cycle Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, Woods87, Guest83]
GO:0006091 - generation of precursor metabolites and energy Inferred by computational analysis [GOA01]
Molecular Function: GO:0004333 - fumarate hydratase activity Author statement Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, vanVugtLussenbu13, Flint94, Tseng01, Flint92]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Lasserre06]
GO:0042803 - protein homodimerization activity Inferred from experiment [Woods88]
GO:0050163 - oxaloacetate tautomerase activity Inferred from experiment [Flint93c]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Flint92]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016836 - hydro-lyase activity Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Lasserre06]

MultiFun Terms: metabolism energy metabolism, carbon TCA cycle

Essentiality data for fumA 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]

Credits:
Last-Curated ? 25-Feb-2013 by Keseler I , SRI International


Enzymatic reaction of: fumarase A

Synonyms: fumarate hydratase

EC Number: 4.2.1.2

(S)-malate <=> fumarate + 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. [vanVugtLussenbu13]

Alternative Substrates for fumarate [Flint94 ]: fluorofumarate [Flint94 ] , acetylenedicarboxylate [Flint94 ]

Alternative Substrates for (S)-malate [Flint94 ]: D-tartrate [Kim07 , Flint94 ]

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

Summary:
Purification to homogeneity of fumarase A was first reported from E. coli W [Ueda91, Yumoto88].

Inhibition of fumarase A activity by Ag+, Hg2+, Cd2+, and Zn2+ is due to damage to the 4Fe-4S cluster [Xu12].

The midpoint potential of FumA at pH 8 is -300 mV [vanVugtLussenbu13].

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Flint92, Flint94]

Inhibitors (Unknown Mechanism): Cd2+ [Xu12] , Zn2+ [Xu12] , Ag+ [Xu12] , Hg2+ [Xu12] , 2-hydroxy-3-nitropropionate [Flint94, Flint92] , superoxide [Flint93b]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Vmax (µmol mg-1 min-1)
Citations
(S)-malate
700.0
3100.0
[Flint92]
(S)-malate
720.0
[vanVugtLussenbu13]
fumarate
600.0
[Flint92]
fumarate
1900.0
[vanVugtLussenbu13]


Enzymatic reaction of: oxaloacetate keto-enol-isomerase (fumarase A)

Synonyms: oxaloacetate tautomerase, OAAKE

EC Number: 5.3.2.2

oxaloacetate <=> enol-oxaloacetate

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

Reversibility of this reaction is unspecified.

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
enol-oxaloacetate
100.0
30.0
[Flint93c]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Link97, UniProt11]
UniProt: Removed.
Chain 2 -> 548
[UniProt09]
UniProt: Fumarate hydratase class I, aerobic;
Metal-Binding-Site 318
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Active-Site 397
[UniProt10]
UniProt: Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 463
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1612 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10356; 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

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

Chen12a: Chen YP, Lin HH, Yang CD, Huang SH, Tseng CP (2012). "Regulatory role of cAMP receptor protein over Escherichia coli fumarase genes." J Microbiol 50(3);426-33. PMID: 22752906

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

Flint92: Flint DH, Emptage MH, Guest JR (1992). "Fumarase a from Escherichia coli: purification and characterization as an iron-sulfur cluster containing enzyme." Biochemistry 31(42);10331-7. PMID: 1329945

Flint93b: Flint DH, Tuminello JF, Emptage MH (1993). "The inactivation of Fe-S cluster containing hydro-lyases by superoxide." J Biol Chem 268(30);22369-76. PMID: 8226748

Flint93c: Flint DH (1993). "Escherichia coli fumarase A catalyzes the isomerization of enol and keto oxalacetic acid." Biochemistry 1993;32(3);799-805. PMID: 8422384

Flint94: Flint DH (1994). "Initial kinetic and mechanistic characterization of Escherichia coli fumarase A." Arch Biochem Biophys 1994;311(2);509-16. PMID: 8203917

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.

Gray66: Gray CT, Wimpenny JW, Mossman MR (1966). "Regulation of metabolism in facultative bacteria. II. Effects of aerobiosis, anaerobiosis and nutrition on the formation of Krebs cycle enzymes in Escherichia coli." Biochim Biophys Acta 117(1);33-41. PMID: 5330664

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

Guest83: Guest JR, Roberts RE (1983). "Cloning, mapping, and expression of the fumarase gene of Escherichia coli K-12." J Bacteriol 153(2);588-96. PMID: 6296045

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

Kim07: Kim OB, Lux S, Unden G (2007). "Anaerobic growth of Escherichia coli on D-tartrate depends on the fumarate carrier DcuB and fumarase, rather than the L-tartrate carrier TtdT and L-tartrate dehydratase." Arch Microbiol 188(6);583-9. PMID: 17643228

Lara06: Lara AR, Leal L, Flores N, Gosset G, Bolivar F, Ramirez OT (2006). "Transcriptional and metabolic response of recombinant Escherichia coli to spatial dissolved oxygen tension gradients simulated in a scale-down system." Biotechnol Bioeng 93(2);372-85. PMID: 16187334

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

Lin12a: Lin HH, Lin CH, Hwang SM, Tseng CP (2012). "High growth rate downregulates fumA mRNA transcription but is dramatically compensated by its mRNA stability in Escherichia coli." Curr Microbiol 64(5);412-7. PMID: 22302452

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Liochev93: Liochev SI, Fridovich I (1993). "Modulation of the fumarases of Escherichia coli in response to oxidative stress." Arch Biochem Biophys 301(2);379-84. PMID: 8460946

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

Miles84: Miles JS, Guest JR (1984). "Complete nucleotide sequence of the fumarase gene fumA, of Escherichia coli." Nucleic Acids Res 12(8);3631-42. PMID: 6328431

Miles84a: Miles JS, Guest JR (1984). "Nucleotide sequence and transcriptional start point of the phosphomannose isomerase gene (manA) of Escherichia coli." Gene 1984;32(1-2);41-8. PMID: 6397402

Ojima08: Ojima Y, Nishioka M, Taya M (2008). "Metabolic alternations in SOD-deficient Escherichia coli cells when cultivated under oxidative stress from photoexcited titanium dioxide." Biotechnol Lett 30(6);1107-13. PMID: 18338221

Park95a: Park SJ, Gunsalus RP (1995). "Oxygen, iron, carbon, and superoxide control of the fumarase fumA and fumC genes of Escherichia coli: role of the arcA, fnr, and soxR gene products." J Bacteriol 1995;177(21);6255-62. PMID: 7592392

Prevost11: Prevost K, Desnoyers G, Jacques JF, Lavoie F, Masse E (2011). "Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage." Genes Dev 25(4);385-96. PMID: 21289064

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

Tseng01: Tseng CP, Yu CC, Lin HH, Chang CY, Kuo JT (2001). "Oxygen- and growth rate-dependent regulation of Escherichia coli fumarase (FumA, FumB, and FumC) activity." J Bacteriol 2001;183(2);461-7. PMID: 11133938

Tseng97: Tseng CP (1997). "Regulation of fumarase (fumB) gene expression in Escherichia coli in response to oxygen, iron and heme availability: role of the arcA, fur, and hemA gene products." FEMS Microbiol Lett 157(1);67-72. PMID: 9418241

Ueda91: Ueda Y, Yumoto N, Tokushige M, Fukui K, Ohya-Nishiguchi H (1991). "Purification and characterization of two types of fumarase from Escherichia coli." J Biochem 109(5);728-33. PMID: 1917897

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.

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."

vanVugtLussenbu13: van Vugt-Lussenburg BM, van der Weel L, Hagen WR, Hagedoorn PL (2013). "Biochemical Similarities and Differences between the Catalytic [4Fe-4S] Cluster Containing Fumarases FumA and FumB from Escherichia coli." PLoS One 8(2);e55549. PMID: 23405168

Woods87: Woods SA, Guest JR (1987). "Differential roles of the Escherichia coli fumarases and fnr-dependent expression of fumarase B and aspartase." FEMS Microbiol Lett 48:219-24.

Woods88: Woods SA, Schwartzbach SD, Guest JR (1988). "Two biochemically distinct classes of fumarase in Escherichia coli." Biochim Biophys Acta 1988;954(1);14-26. PMID: 3282546

Xu12: Xu FF, Imlay JA (2012). "Silver(I), mercury(II), cadmium(II), and zinc(II) target exposed enzymic iron-sulfur clusters when they toxify Escherichia coli." Appl Environ Microbiol 78(10);3614-21. PMID: 22344668

Yumoto88: Yumoto N, Tokushige M (1988). "Characterization of multiple fumarase proteins in Escherichia coli." Biochem Biophys Res Commun 1988;153(3);1236-43. PMID: 3291870

Other References Related to Gene Regulation

Masse05: Masse E, Vanderpool CK, Gottesman S (2005). "Effect of RyhB small RNA on global iron use in Escherichia coli." J Bacteriol 187(20);6962-71. PMID: 16199566

Spiro91: Spiro S, Guest JR (1991). "Adaptive responses to oxygen limitation in Escherichia coli." Trends Biochem Sci 1991;16(8);310-4. PMID: 1957353

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


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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 Mon Dec 22, 2014, biocyc12.