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Escherichia coli K-12 substr. MG1655 Enzyme: fructose bisphosphate aldolase class I

Gene: fbaB Accession Numbers: G7129 (EcoCyc), b2097, ECK2090

Synonyms: dhnA

Regulation Summary Diagram

Regulation summary diagram for fbaB

Subunit composition of fructose bisphosphate aldolase class I = [FbaB]10
         fructose bisphosphate aldolase monomer = FbaB

This enzyme catalyzes a reversible aldol cleavage/condensation reaction during glycolysis and gluconeogenesis in E. coli. In the glycolytic direction fructose 1,6-bisphosphate (FBP) is cleaved to produce glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (glycerone phosphate).

Two types of FBP aldolases have been distinguished, Class I and Class II. Class I FBP aldolases utilize an active site lysine residue to form a Schiff-base between the ε-amino group of lysine and the carbonyl group of the substrate. They also vary in subunit stoichiometry. Class II FBP aldolases are dimeric and utilize a divalent metal ion in catalysis via a similar mechanism. The Class I enzymes of eukaryotes have been well studied [Thomson98, Baldwin78, Baldwin78a, Stribling73, Alefounder89].

E. coli is one of a few organisms that expresses both classes of FBP aldolase [Stribling73, Baldwin78a]. The Class I enzyme encoded by fbaB is induced by gluconeogenic substrates, whereas the Class II enzyme encoded by fbaA is constitutive. When E. coli K-12 is grown on C-3 carbon sources both classes of aldolase are present, although the Class I enzyme is present only under these conditions. Therefore the Class I enzyme is most likely involved in gluconeogenesis and the Class II enzyme in glycolysis [Scamuffa80].

In earlier work it was thought that the Class I E. coli aldolase was a tetramer [Stribling73]|, but later studies showed that it is a decamer with an apparent molecular mass of 340,000 [Baldwin78a, Thomson98].

The E. coli Class I enzyme has been cloned, overexpressed and characterized. It shows low amino acid sequence identity with other Class I and Class II FBP aldolases from prokaryotes or eukaryotes. In the active site Lys236 was identified as the Schiff-base forming residue, and Lys238 is implicated in substrate binding [Thomson98].

Using a pull-down assay and stationary phase cells, FbaB was one of five proteins found to form a complex with E. coli inorganic pyrophosphatase [Rodina11].

Review: [Perham90]

Locations: cytosol, membrane

Map Position: [2,175,534 <- 2,176,586] (46.89 centisomes, 169°)
Length: 1053 bp / 350 aa

Molecular Weight of Polypeptide: 38.109 kD (from nucleotide sequence), 36.0 kD (experimental) [Thomson98]

Molecular Weight of Multimer: 340.0 kD (experimental) [Thomson98]

Unification Links: ASAP:ABE-0006941, DIP:DIP-36197N, EchoBASE:EB3815, EcoGene:EG14062, EcoliWiki:b2097, ModBase:P0A991, OU-Microarray:b2097, PortEco:fbaB, PR:PRO_000022575, Pride:P0A991, Protein Model Portal:P0A991, RefSeq:NP_416600, RegulonDB:G7129, SMR:P0A991, String:511145.b2097, UniProt:P0A991

Relationship Links: InterPro:IN-FAMILY:IPR002915, InterPro:IN-FAMILY:IPR013785, Pfam:IN-FAMILY:PF01791

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for fbaB

GO Terms:
Biological Process:
Inferred by computational analysisGO:0006096 - glycolytic process [UniProtGOA11a]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0004332 - fructose-bisphosphate aldolase activity [GOA01, Thomson98]
Inferred from experimentGO:0005515 - protein binding [Rodina11]
Inferred from experimentGO:0042802 - identical protein binding [Thomson98, Lasserre06]
Inferred by computational analysisGO:0003824 - catalytic activity [GOA01a]
Inferred by computational analysisGO:0016829 - lyase activity [UniProtGOA11a, GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, Lasserre06]
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolismenergy metabolism, carbonglycolysis

Essentiality data for fbaB 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]

Last-Curated 06-Mar-2015 by Fulcher C, SRI International

Enzymatic reaction of: fructose bisphosphate aldolase

Inferred from experiment

EC Number:

fructose 1,6-bisphosphate ⇄ glycerone phosphate + D-glyceraldehyde 3-phosphate

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

This reaction is reversible. [Thomson98]

Alternative Substrates for fructose 1,6-bisphosphate: D-fructose 1-phosphate [Baldwin78a]

In Pathways: superpathway of hexitol degradation (bacteria), superpathway of glycolysis and Entner-Doudoroff, superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass, gluconeogenesis I, glycolysis II (from fructose 6-phosphate), glycolysis I (from glucose 6-phosphate)

Reduction by borohydride in the presence of fructose 1,6-bisphosphate or dihydroxyacetone phosphate irreversibly inhibits the enzyme. EDTA is not a inhibitor. Activation by several compounds tested was strongly pH-dependent. Fructose 1-phosphate is slowly cleaved and is not affected by activator compounds [Baldwin78a]]|.

The enzymes described in [Stribling73, Baldwin78a] refer to E. coli (Crookes' strain).

Activators (Unknown Mechanism): 2-oxoglutarate [Baldwin78a], citrate [Baldwin78a], phosphoenolpyruvate [Baldwin78a], sn-glycerol 3-phosphate [Baldwin78a] Inhibitors (Irreversible): borohydride [Baldwin78a]Kinetic Parameters:
Substrate Km (μM) kcat (sec-1) kcat/Km (sec-1 μM-1) Citations
fructose 1,6-bisphosphate 20.0 13.0 0.65 [Thomson98]

Sequence Features

Protein sequence of fructose bisphosphate aldolase monomer with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Inferred from experiment[Thomson98]
UniProt: Removed.
Chain 2 -> 350
Author statement[UniProt15]
UniProt: Fructose-bisphosphate aldolase class 1.
Pfam PF01791 69 -> 326
Inferred by computational analysis[Finn14]
DeoC : DeoC/LacD family aldolase
Sequence-Conflict 192
Inferred by curator[UniProt15]
UniProt: (in Ref. 1; AAB18249).
N6-acetyllysine-Modification 208
Inferred from experiment[Zhang09a]
UniProt: N6-acetyllysine.
Mutagenesis-Variant 237
Author statement[UniProt15]
UniProt: Loss of activity.
Active-Site 237
Author statement[UniProt15]
UniProt: Schiff-base intermediate with dihydroxyacetone-P.
Mutagenesis-Variant 239
Author statement[UniProt15]
UniProt: No change in activity.
N6-acetyllysine-Modification 262
Inferred from experiment[Zhang09a]
UniProt: N6-acetyllysine.
Sequence-Conflict 309
Inferred by curator[UniProt15]
UniProt: (in Ref. 1; AAB18249).

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

Gene local context diagram

Transcription Unit

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Alefounder89: Alefounder PR, Baldwin SA, Perham RN, Short NJ (1989). "Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli." Biochem J 1989;257(2);529-34. PMID: 2649077

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

Baldwin78: Baldwin SA, Perham RN, Stribling D (1978). "Purification and characterization of the class-II D-fructose 1,6-bisphosphate aldolase from Escherichia coli (Crookes' strain)." Biochem J 1978;169(3);633-41. PMID: 417719

Baldwin78a: Baldwin SA, Perham RN (1978). "Novel kinetic and structural properties of the class-I D-fructose 1,6-bisphosphate aldolase from Escherichia coli (Crookes' strain)." Biochem J 1978;169(3);643-52. PMID: 348198

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."

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

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

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

Perham90: Perham RN (1990). "The fructose-1,6-bisphosphate aldolases: same reaction, different enzymes." Biochem Soc Trans 18(2);185-7. PMID: 2199259

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Rodina11: Rodina E, Vorobieva N, Kurilova S, Mikulovich J, Vainonen J, Aro EM, Nazarova T (2011). "Identification of new protein complexes of Escherichia coli inorganic pyrophosphatase using pull-down assay." Biochimie 93(9);1576-83. PMID: 21664227

Scamuffa80: Scamuffa MD, Caprioli RM (1980). "Comparison of the mechanisms of two distinct aldolases from Escherichia coli grown on gluconeogenic substrates." Biochim Biophys Acta 1980;614(2);583-90. PMID: 6996735

Stribling73: Stribling D, Perham RN (1973). "Purification and characterization of two fructose diphosphate aldolases from Escherichia coli (Crookes' strain)." Biochem J 1973;131(4);833-41. PMID: 4198624

Thomson98: Thomson GJ, Howlett GJ, Ashcroft AE, Berry A (1998). "The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase." Biochem J 1998;331 ( Pt 2);437-45. PMID: 9531482

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Zhang09a: 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

Lacour04: Lacour S, Landini P (2004). "SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences." J Bacteriol 186(21);7186-95. PMID: 15489429

Shimada11: Shimada T, Yamamoto K, Ishihama A (2011). "Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli." J Bacteriol 193(3);649-59. PMID: 21115656

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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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