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



Gene: fumB Accession Numbers: EG10357 (EcoCyc), b4122, ECK4115

Regulation Summary Diagram: ?

Subunit composition of fumarase B = [FumB]2
         fumarase B monomer = FumB

Summary:
Fumarase B (FumB) is one of three fumarase isozymes participating in the TCA cycle. FumB belongs to the class I fumarases; like FumA, it is a homodimeric 4Fe-4S cluster-containing protein [Woods88, vanVugtLussenbu13]. Fumarase B is required for anaerobic growth on D-tartrate [Kim07] and appears to be involved in biofilm formation [Herzberg06].

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 [Flint93a]. Although FumB was previously reported to have a higher affinity for malate than for fumarate [Woods88], recent kinetic data using a purified enzyme have shown it to be similar to FumA [vanVugtLussenbu13]. FumB is thought to function as an alternative enzyme during anaerobiosis [Woods87, Tseng01]. 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. [Tseng97, Liochev93, Tseng01, Lara06]

Expression of all three fumarase genes is anaerobically controlled. Expression of fumB gene 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.

Overexpression of fumB complements the fumA1 mutation [Guest83a, Guest85a] and a fumAC deletion [Henson87]. The expression level of fumB is highest under anaerobic growth on glycerol and fumarate [Woods87]. fumB expression is regulated in response to oxygen, iron and heme availability [Gruer94, Tseng97] and increases 9-fold upon deletion of tqsA, which increases biofilm formation [Herzberg06].

Citations: [Bell89, Gray66, Guest92, Overton06]

Gene Citations: [AboAmer04, Golby98, Bell89]

Locations: cytosol

Map Position: [4,343,703 <- 4,345,349] (93.62 centisomes)
Length: 1647 bp / 548 aa

Molecular Weight of Polypeptide: 60.105 kD (from nucleotide sequence), 61.0 kD (experimental) [Guest85a ]

Molecular Weight of Multimer: 120.0 kD (experimental) [vanVugtLussenbu13]

Isozyme Sequence Similarity:
fumarase A monomer: YES

Unification Links: ASAP:ABE-0013501 , CGSC:18289 , EchoBASE:EB0352 , EcoGene:EG10357 , EcoliWiki:b4122 , OU-Microarray:b4122 , PortEco:fumB , PR:PRO_000022735 , Pride:P14407 , Protein Model Portal:P14407 , RefSeq:NP_418546 , RegulonDB:EG10357 , SMR:P14407 , String:511145.b4122 , UniProt:P14407

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, Guest85a]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0042710 - biofilm formation Inferred from experiment [Herzberg06]
GO:0006091 - generation of precursor metabolites and energy Inferred by computational analysis [GOA01]
Molecular Function: GO:0004333 - fumarate hydratase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, vanVugtLussenbu13, Flint93a]
GO:0042803 - protein homodimerization activity Inferred from experiment [vanVugtLussenbu13]
GO:0047808 - D(-)-tartrate dehydratase activity Inferred from experiment [vanVugtLussenbu13, Kim07]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, vanVugtLussenbu13]
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 fermentation
metabolism energy metabolism, carbon TCA cycle

Essentiality data for fumB 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 B

Synonyms: fumarate hydratase B

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]

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 of fumarase B from E. coli W has been described [Yumoto88].

The midpoint potential of FumB at pH 8 is -283 mV [vanVugtLussenbu13].

Inhibitors (Unknown Mechanism): superoxide [Flint93a, Korshunov02]

Kinetic Parameters:

Substrate
Km (μM)
Vmax (µmol mg-1 min-1)
Citations
(S)-malate
300.0
490.0
[vanVugtLussenbu13]
fumarate
320.0
1430.0
[vanVugtLussenbu13]


Enzymatic reaction of: D-tartrate dehydratase (fumarase B)

EC Number: 4.2.1.81

D-tartrate <=> oxaloacetate + H2O

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)
Vmax (µmol mg-1 min-1)
Citations
D-tartrate
800.0
9.2
[vanVugtLussenbu13]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 50
[Bell89, UniProt10]
Alternate sequence: L → V; UniProt: (in Ref. 1; AAA23827);
Acetylation-Modification 192
[Zhang09, UniProt11]
UniProt: N6-acetyllysine.
Metal-Binding-Site 318
[UniProt10a]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Active-Site 397
[UniProt10a]
UniProt: Non-Experimental Qualifier: potential;
Amino-Acid-Sites-That-Bind 463
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4122 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10357; confirmed by SwissProt match.


References

AboAmer04: Abo-Amer AE, Munn J, Jackson K, Aktas M, Golby P, Kelly DJ, Andrews SC (2004). "DNA interaction and phosphotransfer of the C4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli." J Bacteriol 186(6);1879-89. PMID: 14996819

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

Bell89: Bell PJ, Andrews SC, Sivak MN, Guest JR (1989). "Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12." J Bacteriol 1989;171(6);3494-503. PMID: 2656658

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

Flint93a: 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

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.

Golby98: Golby P, Kelly DJ, Guest JR, Andrews SC (1998). "Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli." J Bacteriol 1998;180(24);6586-96. PMID: 9852003

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

Guest83a: 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

Guest85a: Guest JR, Miles JS, Roberts RE, Woods SA (1985). "The fumarase genes of Escherichia coli: location of the fumB gene and discovery of a new gene (fumC)." J Gen Microbiol 131(11);2971-84. PMID: 3005475

Guest92: Guest JR, Russell GC (1992). "Complexes and complexities of the citric acid cycle in Escherichia coli." Curr Top Cell Regul 33;231-47. PMID: 1499335

Henson87: Henson JM, Blake NK, Marek LE (1987). "The isolation of fumB mutants of Escherichia coli." J Gen Microbiol 133(9);2631-8. PMID: 2834509

Herzberg06: Herzberg M, Kaye IK, Peti W, Wood TK (2006). "YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport." J Bacteriol 188(2);587-98. PMID: 16385049

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

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

Korshunov02: Korshunov SS, Imlay JA (2002). "A potential role for periplasmic superoxide dismutase in blocking the penetration of external superoxide into the cytosol of Gram-negative bacteria." Mol Microbiol 43(1);95-106. PMID: 11849539

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

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

Overton06: Overton TW, Griffiths L, Patel MD, Hobman JL, Penn CW, Cole JA, Constantinidou C (2006). "Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology." Biochem Soc Trans 34(Pt 1);104-7. PMID: 16417494

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

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

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."

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

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

Zhang09: 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

Baez13a: 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

Chen12: 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

Janausch04: Janausch IG, Garcia-Moreno I, Lehnen D, Zeuner Y, Unden G (2004). "Phosphorylation and DNA binding of the regulator DcuR of the fumarate-responsive two-component system DcuSR of Escherichia coli." Microbiology 150(Pt 4);877-83. PMID: 15073297

Kim09e: Kim OB, Reimann J, Lukas H, Schumacher U, Grimpo J, Dunnwald P, Unden G (2009). "Regulation of tartrate metabolism by TtdR and relation to the DcuS-DcuR-regulated C4-dicarboxylate metabolism of Escherichia coli." Microbiology 155(Pt 11);3632-40. PMID: 19661178

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

Scheu12: Scheu PD, Witan J, Rauschmeier M, Graf S, Liao YF, Ebert-Jung A, Basche T, Erker W, Unden G (2012). "CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo." J Bacteriol 194(3);636-45. PMID: 22101843

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


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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 Tue Nov 25, 2014, BIOCYC13A.