|Gene:||fbaA||Accession Numbers: EG10282 (EcoCyc), b2925, ECK2921|
Synonyms: ald, fba, fda
Subunit composition of
fructose bisphosphate aldolase class II = [FbaA]2
fructose bisphosphate aldolase monomer = FbaA
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, Baldwin78a, Baldwin78, Stribling73, Alefounder89a].
E. coli is one of a few organisms that expresses both classes of FBP aldolase [Stribling73, Baldwin78]. 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].
The E. coli enzyme resembles the typical class II aldolase from yeast in size and amino acid composition, strongly suggesting that they are related. These aldolases are found both in the eukaryotic green algae and fungi, and in the prokaryotic cyanobacteria and other bacteria [Baldwin78a].
A number of studies provided initial characterizations of the enzyme including mutant phenotypes [Bock66a, Bock66, Schreyer73, Su75, Irani77], gene localization [Ruffler73, Alefounder89], its metabolic regulation [Thomas72, Babul93], and evidence for its modification by phosphate [Babul88] and 2-mercaptoethanol [Packman95].
The enzyme has been cloned, overexpressed and purified in high yield [Henderson94]. Like other Class II enzymes, FbaA requires a divalent metal ion for activity. Zn2+ is isolated with the enzyme, but several other metal ions including Co2+, Fe2+ and Mn2+ can form an active metalloprotein complex [Scamuffa80]. His108 and His111 were identified as the zinc-binding ligands [Berry93]. The Arg331 residue is involved in substrate binding [Qamar96]. Asn286, Asp109 [Plater99], Asn35, Ser61, Lys325 [Zgiby00], and Glu182 [Zgiby02] also have roles in catalysis. A reaction mechanism has been proposed based on NMR spectroscopic data that involves an enzyme-bound enediol(ate) form of dihydroxyacetone phosphate as an intermediate [Szwergold95].
Following initial crystallization studies [Naismith92, Kitagawa95], crystal structures of the enzyme have been solved at 1.67 and 2.50 Å resolution [Blom96, Cooper96]. Crystal structures were also solved at 2.0 Å resolution in complex with phosphoglycolohydroxamate [Hall99], and with Cd2+ replacing Zn2+ at the active site [Hall03].
The ts8 and h8 mutations cause temperature-sensitive growth and inhibit stable RNA synthesis at the non-permissive temperature. Both mutations are located in the fbaA gene [Singer91a, Singer91]. The ts8 mutation was also shown to destabilize ptsG mRNA at the nonpermissive temperature [Morita03].
An fda mutant exhibits a heat-sensitive defect in rRNA transcription that is elicited via altered abundance of ppGpp and of initiating NTPs [Schneider03].
Directed evolution studies have resulted in fructose bisphosphate aldolase variants with increased temperature and organic solvent stability [Hao04]. The enzyme has also been engineered for increased activity toward N-Cbz-aminoaldehyde derivatives [Gutierrez11].
Competitive phosphoglycolosulfamate inhibitors of of the E. coli enzyme have been synthesized [Gavalda05]. Nickel toxicity in E. coli has been shown to be due to binding of nickel to the non-catalytic zinc site [Macomber11].
An NMR spectroscopy technique has been used for relaxation measurements of the E. coli enzyme [Burnley07].
A series of vectors inducibly expressing paired-terminus antisense RNAs was constructed to silence central carbon metabolism in host E. coli K-12 MG1655. A vector that silenced fbaA at 81% efficacy did not cause severe growth inhibition [Nakashima14].
Gene Citations: [Bardey05]
|Map Position: [3,068,187 <- 3,069,266] (66.13 centisomes, 238°)||Length: 1080 bp / 359 aa|
Molecular Weight of Polypeptide: 39.147 kD (from nucleotide sequence), 40.0 kD (experimental) [Alefounder89a ]
Molecular Weight of Multimer: 78.0 kD (experimental) [Berry93]
Unification Links: ASAP:ABE-0009600 , CGSC:786 , DIP:DIP-31872N , EchoBASE:EB0278 , EcoGene:EG10282 , EcoliWiki:b2925 , OU-Microarray:b2925 , PortEco:fbaA , PR:PRO_000022574 , Pride:P0AB71 , Protein Model Portal:P0AB71 , RefSeq:NP_417400 , RegulonDB:EG10282 , SMR:P0AB71 , String:511145.b2925 , UniProt:P0AB71
Relationship Links: InterPro:IN-FAMILY:IPR000771 , InterPro:IN-FAMILY:IPR006411 , InterPro:IN-FAMILY:IPR013785 , PDB:Structure:1B57 , PDB:Structure:1DOS , PDB:Structure:1GYN , PDB:Structure:1ZEN , Pfam:IN-FAMILY:PF01116 , Prosite:IN-FAMILY:PS00602 , Prosite:IN-FAMILY:PS00806
In Paralogous Gene Group: 346 (4 members)
|Biological Process:||GO:0006096 - glycolytic process
[UniProtGOA12, UniProtGOA11a, GOA01a, Bock66a]
GO:0005975 - carbohydrate metabolic process [GOA01a]
|Molecular Function:||GO:0004332 - fructose-bisphosphate aldolase activity
[GOA01, GOA01a, Berry93, Scamuffa80, Bock66a]
GO:0005515 - protein binding [Butland05]
GO:0008270 - zinc ion binding [GOA01a, Berry93, Katayama02]
GO:0042803 - protein homodimerization activity [Berry93]
GO:0003824 - catalytic activity [GOA01a]
GO:0016829 - lyase activity [UniProtGOA11a]
GO:0016832 - aldehyde-lyase activity [GOA01a]
GO:0046872 - metal ion binding [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol [Ishihama08, LopezCampistrou05]|
|MultiFun Terms:||metabolism → carbon utilization → carbon compounds|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Enzymatic reaction of: fructose bisphosphate aldolase
Synonyms: fructose-1,6-bisphosphate aldolase, fructose-1,6-bisphosphate triosephosphate lyase
EC Number: 126.96.36.199
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.
This reaction is reversible. [Morse68]
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)
Activation of the E. coli enzyme by NH4+ or K+ was cited in [Blom96] as a personal communication.
Enzymatic reaction of: sedoheptulose bisphosphate aldolase (fructose bisphosphate aldolase class II)
EC Number: 4.1.2.-
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.
The reaction is favored in the opposite direction.
In Pathways: sedoheptulose bisphosphate bypass
|Chain||2 -> 359|
|Protein-Segment||266 -> 268|
|Protein-Segment||287 -> 290|
10/20/97 Gene b2925 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10282; confirmed by SwissProt match.
Alefounder89: Alefounder PR, Perham RN (1989). "Identification, molecular cloning and sequence analysis of a gene cluster encoding the class II fructose 1,6-bisphosphate aldolase, 3-phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli." Mol Microbiol 3(6);723-32. PMID: 2546007
Alefounder89a: 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 (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
Baldwin78a: 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
Bardey05: Bardey V, Vallet C, Robas N, Charpentier B, Thouvenot B, Mougin A, Hajnsdorf E, Regnier P, Springer M, Branlant C (2005). "Characterization of the molecular mechanisms involved in the differential production of erythrose-4-phosphate dehydrogenase, 3-phosphoglycerate kinase and class II fructose-1,6-bisphosphate aldolase in Escherichia coli." Mol Microbiol 57(5);1265-87. PMID: 16102000
Burnley07: Burnley BT, Kalverda AP, Paisey SJ, Berry A, Homans SW (2007). "Hadamard NMR spectroscopy for relaxation measurements of large (>35 kDa) proteins." J Biomol NMR 39(3);239-45. PMID: 17882509
Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043
Cooper96: Cooper SJ, Leonard GA, McSweeney SM, Thompson AW, Naismith JH, Qamar S, Plater A, Berry A, Hunter WN (1996). "The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold." Structure 4(11);1303-15. PMID: 8939754
Gavalda05: Gavalda S, Braga R, Dax C, Vigroux A, Blonski C (2005). "N-Sulfonyl hydroxamate derivatives as inhibitors of class II fructose-1,6-diphosphate aldolase." Bioorg Med Chem Lett 15(24);5375-7. PMID: 16236509
Gutierrez11: Gutierrez M, Parella T, Joglar J, Bujons J, Clapes P (2011). "Structure-guided redesign of D-fructose-6-phosphate aldolase from E. coli: remarkable activity and selectivity towards acceptor substrates by two-point mutation." Chem Commun (Camb) 47(20);5762-4. PMID: 21499643
Hall03: Hall DR, Kemp LE, Leonard GA, Marshall K, Berry A, Hunter WN (2003). "The organization of divalent cations in the active site of cadmium Escherichia coli fructose-1,6-bisphosphate aldolase." Acta Crystallogr D Biol Crystallogr 59(Pt 3);611-4. PMID: 12595741
Hall99: Hall DR, Leonard GA, Reed CD, Watt CI, Berry A, Hunter WN (1999). "The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity." J Mol Biol 287(2);383-94. PMID: 10080900
Hao04: Hao J, Berry A (2004). "A thermostable variant of fructose bisphosphate aldolase constructed by directed evolution also shows increased stability in organic solvents." Protein Eng Des Sel 17(9);689-97. PMID: 15531627
Henderson94: Henderson I, Garcia-Junceda E, Liu KK, Chen YL, Shen GJ, Wong CH (1994). "Cloning, overexpression and isolation of the type II FDP aldolase from E. coli for specificity study and synthetic application." Bioorg Med Chem 2(8);837-43. PMID: 7894977
Kitagawa95: Kitagawa Y, Leonard GA, Harrop SJ, Peterson MR, Hunter WN, Qamar S, Berry A (1995). "Additional crystal forms of the E. coli class II fructose-1,6-bisphosphate aldolase." Acta Crystallogr D Biol Crystallogr 51(Pt 5);833-4. PMID: 15299818
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
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
Macomber11: Macomber L, Elsey SP, Hausinger RP (2011). "Fructose-1,6-bisphosphate aldolase (class II) is the primary site of nickel toxicity in Escherichia coli." Mol Microbiol 82(5);1291-300. PMID: 22014167
Morita03: Morita T, El-Kazzaz W, Tanaka Y, Inada T, Aiba H (2003). "Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli." J Biol Chem 278(18);15608-14. PMID: 12578824
Naismith92: Naismith JH, Ferrara JD, Bailey S, Marshall K, Dauter Z, Wilson KS, Habash J, Harrop SJ, Berry AJ, Hunter WN (1992). "Initiating a crystallographic study of a class II fructose-1,6-bisphosphate aldolase." J Mol Biol 225(4);1137-41. PMID: 1613797
Nakahigashi09: Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M (2009). "Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism." Mol Syst Biol 5;306. PMID: 19756045
Nakashima14: Nakashima N, Ohno S, Yoshikawa K, Shimizu H, Tamura T (2014). "A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli." Appl Environ Microbiol 80(2);564-73. PMID: 24212579
Packman95: Packman LC, Berry A (1995). "A reactive, surface cysteine residue of the class-II fructose-1,6-bisphosphate aldolase of Escherichia coli revealed by electrospray ionisation mass spectrometry." Eur J Biochem 227(1-2);510-5. PMID: 7851430
Peng11: Peng C, Lu Z, Xie Z, Cheng Z, Chen Y, Tan M, Luo H, Zhang Y, He W, Yang K, Zwaans BM, Tishkoff D, Ho L, Lombard D, He TC, Dai J, Verdin E, Ye Y, Zhao Y (2011). "The first identification of lysine malonylation substrates and its regulatory enzyme." Mol Cell Proteomics 10(12);M111.012658. PMID: 21908771
Qamar96: Qamar S, Marsh K, Berry A (1996). "Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli." Protein Sci 5(1);154-61. PMID: 8771208
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
Schneider03: Schneider DA, Gourse RL (2003). "Changes in the concentrations of guanosine 5'-diphosphate 3'-diphosphate and the initiating nucleoside triphosphate account for inhibition of rRNA transcription in fructose-1,6-diphosphate aldolase (fda) mutants." J Bacteriol 185(20);6192-4. PMID: 14526031
Singer91: Singer M, Rossmiessl P, Cali BM, Liebke H, Gross CA (1991). "The Escherichia coli ts8 mutation is an allele of fda, the gene encoding fructose-1,6-diphosphate aldolase." J Bacteriol 173(19);6242-8. PMID: 1917856
Singer91a: Singer M, Walter WA, Cali BM, Rouviere P, Liebke HH, Gourse RL, Gross CA (1991). "Physiological effects of the fructose-1,6-diphosphate aldolase ts8 mutation on stable RNA synthesis in Escherichia coli." J Bacteriol 173(19);6249-57. PMID: 1717436
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
Thomas72: Thomas AD, Doelle HW, Westwood AW, Gordon GL (1972). "Effect of oxygen on several enzymes involved in the aerobic and anaerobic utilization of glucose in Escherichia coli." J Bacteriol 112(3);1099-105. PMID: 4344916
Wilkins98: Wilkins MR, Gasteiger E, Tonella L, Ou K, Tyler M, Sanchez JC, Gooley AA, Walsh BJ, Bairoch A, Appel RD, Williams KL, Hochstrasser DF (1998). "Protein identification with N and C-terminal sequence tags in proteome projects." J Mol Biol 278(3);599-608. PMID: 9600841
Zgiby00: Zgiby SM, Thomson GJ, Qamar S, Berry A (2000). "Exploring substrate binding and discrimination in fructose1, 6-bisphosphate and tagatose 1,6-bisphosphate aldolases." Eur J Biochem 267(6);1858-68. PMID: 10712619
Zgiby02: Zgiby S, Plater AR, Bates MA, Thomson GJ, Berry A (2002). "A functional role for a flexible loop containing Glu182 in the class II fructose-1,6-bisphosphate aldolase from Escherichia coli." J Mol Biol 315(2);131-40. PMID: 11779234
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
Charpentier98: Charpentier B, Bardey V, Robas N, Branlant C (1998). "The EIIGlc protein is involved in glucose-mediated activation of Escherichia coli gapA and gapB-pgk transcription." J Bacteriol 1998;180(24);6476-83. PMID: 9851989
Olvera09: Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolivar F (2009). "Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation." PLoS One 4(10);e7466. PMID: 19838295
Ramseier95a: Ramseier TM, Bledig S, Michotey V, Feghali R, Saier MH (1995). "The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli." Mol Microbiol 1995;16(6);1157-69. PMID: 8577250
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