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



Gene: fbaA Accession Numbers: EG10282 (EcoCyc), b2925, ECK2921

Synonyms: ald, fba, fda

Regulation Summary Diagram: ?

Subunit composition of fructose bisphosphate aldolase class II = [FbaA]2
         fructose bisphosphate aldolase monomer = FbaA

Summary:
Fructose bisphosphate aldolase (FbaA) is one of the reversible enzyme of the glycolysis pathway. It belongs to the Class II fructose-1,6-bisphosphate aldolases. In relation to the Class I enzymes (primarily studied and found in eukaryotes), comparatively little is known about the class II enzymes [Alefounder89]. When E. coli K-12 is grown on C-3 carbon sources both classes of aldolase are present. However 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 with glycolysis [Scamuffa80].

Like other Class II enzymes, FbaA requires a divalent metal ion for activity [Scamuffa80]. Zinc is isolated with the enzyme, but several other metal ions including cobalt, iron and manganese can form an active metallo-protein complex [Scamuffa80]. His108 and His111 were identified as the zinc-binding ligands [Berry93]. The Arg331 residue is involved in substrate binding [Qamar96].

A reaction mechanism has been proposed [Szwergold95].

Crystal structures of the enzyme have been solved [Blom96].

The E. coli enzyme resembles the typical class II aldolase from yeast in size and amino acid composition. This is a strong suggestion that they are related [Baldwin78a]. These less well studied aldolases are found both in the eukaryotic green algae and fungi, and in the prokaryotic blue-green algae and bacteria [Baldwin78a].

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].

An fda mutant exhibits a heat-sensitive defect in rRNA transcription that is elicited via altered abundance of ppGpp and of initiating NTPs [Schneider03].

Review: [Perham90]

Citations: [Bock66a, Bock66, Thomas72, Schreyer73, Ruffler73, Su75, Babul88, Irani77, Alefounder89a, Naismith92, Babul93, Packman95, Kitagawa95]

Gene Citations: [Alefounder89a, Bardey05]

Locations: cytosol

Map Position: [3,068,187 <- 3,069,266] (66.13 centisomes)
Length: 1080 bp / 359 aa

Molecular Weight of Polypeptide: 39.147 kD (from nucleotide sequence), 40.0 kD (experimental) [Alefounder89 ]

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)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006096 - glycolytic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA01a, Bock66a]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0004332 - fructose-bisphosphate aldolase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Scamuffa80, Bock66a]
GO:0005515 - protein binding Inferred from experiment [Butland05]
GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA01a, Berry93, Katayama02]
GO:0042803 - protein homodimerization activity Inferred from experiment [Berry93]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016832 - aldehyde-lyase activity Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for fbaA knockouts: ?

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: 4.1.2.13

fructose 1,6-bisphosphate <=> dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate

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.

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-6P) , glycolysis I (from glucose-6P)

Summary:
The enzymes described in [Stribling73, Baldwin78a] were purified from E. coli Crookes' strain.

Citations: [Henderson94]

Cofactors or Prosthetic Groups: Zn2+ [Berry93, Scamuffa80]

Activators (Unknown Mechanism): K+

Inhibitors (Unknown Mechanism): EDTA [Stribling73]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
fructose 1,6-bisphosphate
240.0
10.33
[Berry93]


Enzymatic reaction of: sedoheptulose bisphosphate aldolase (fructose bisphosphate aldolase class II)

EC Number: 4.1.2.-

dihydroxyacetone phosphate + D-erythrose 4-phosphate <=> D-sedoheptulose-1,7-bisphosphate

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


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Alefounder89, Wilkins98, Link97, UniProt11]
UniProt: Removed.
Chain 2 -> 359
[UniProt09]
UniProt: Fructose-bisphosphate aldolase class 2;
N6-succinyllysine-Modification 9
[Peng11, Zhang11, UniProt12b]
UniProt: N6-succinyllysine; alternate.
Acetylation-Modification 9
[Zhang09, UniProt12b]
UniProt: N6-acetyllysine; alternate.
Mutagenesis-Variant 36
[Zgiby00, UniProt11]
Alternate sequence: N → A; UniProt: 1.5% of wild-type activity. 5-fold decrease in FBP affinity.
Mutagenesis-Variant 60
[Zgiby00, UniProt11]
Alternate sequence: Q → A; UniProt: 81% of wild-type activity. 1.3-fold decrease in FBP affinity.
Mutagenesis-Variant 62
[Zgiby00, UniProt11]
Alternate sequence: S → T; UniProt: 60% of wild-type activity. 2.5-fold decrease in FBP affinity.
Alternate sequence: S → A; UniProt: 8% of wild-type activity. 16-fold decrease in FBP affinity.
Amino-Acid-Sites-That-Bind 62
[UniProt10a]
UniProt: Glyceraldehyde 3-phosphate; Non-Experimental Qualifier: probable;
N6-succinyllysine-Modification 72
[Zhang11, UniProt12b]
UniProt: N6-succinyllysine.
Mutagenesis-Variant 108
[Berry93, UniProt11]
Alternate sequence: H → A; UniProt: Loss of activity.
Active-Site 110
[Hall99a, UniProt11]
UniProt: Proton donor.
Mutagenesis-Variant 111
[Berry93, UniProt11]
Alternate sequence: H → A; UniProt: Loss of activity.
Metal-Binding-Site 111
[UniProt10]
UniProt: Zinc 1; catalytic;
Mutagenesis-Variant 112
[Berry93, UniProt11]
Alternate sequence: C → A; UniProt: Partial loss of activity.
N6-succinyllysine-Modification 115
[Zhang11, UniProt12b]
UniProt: N6-succinyllysine.
Metal-Binding-Site 145
[UniProt10]
UniProt: Zinc 2;
Metal-Binding-Site 175
[UniProt10]
UniProt: Zinc 2;
Metal-Binding-Site 227
[UniProt10]
UniProt: Zinc 1; catalytic;
Amino-Acid-Sites-That-Bind 228
[UniProt10]
UniProt: Dihydroxyacetone phosphate; via amide nitrogen;
N6-succinyllysine-Modification 231
[Zhang11, UniProt12b]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 251
[Zhang11, UniProt12b]
UniProt: N6-succinyllysine.
Metal-Binding-Site 265
[UniProt10]
UniProt: Zinc 1; catalytic;
Protein-Segment 266 -> 268
[UniProt10a]
UniProt: Dihydroxyacetone phosphate binding; Sequence Annotation Type: region of interest;
Protein-Segment 287 -> 290
[UniProt10a]
UniProt: Dihydroxyacetone phosphate binding; Sequence Annotation Type: region of interest;
N6-succinyllysine-Modification 319
[Zhang11, UniProt12b]
UniProt: N6-succinyllysine.
N6-succinyllysine-Modification 326
[Zhang11, UniProt12b]
UniProt: N6-succinyllysine.
Mutagenesis-Variant 326
[Zgiby00, UniProt11]
Alternate sequence: K → A; UniProt: 6% of wild-type activity. 2.2-fold decrease in FBP affinity.
N6-succinyllysine-Modification 348
[Zhang11, UniProt12b]
UniProt: N6-succinyllysine.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2925 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10282; confirmed by SwissProt match.


References

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

Alefounder89a: 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

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

Babul88: Babul J, Fraenkel DG (1988). "Phosphate modification of fructose-1,6-bisphosphate aldolase in Escherichia coli." Biochem Biophys Res Commun 151(3);1033-8. PMID: 3281666

Babul93: Babul J, Clifton D, Kretschmer M, Fraenkel DG (1993). "Glucose metabolism in Escherichia coli and the effect of increased amount of aldolase." Biochemistry 32(17);4685-92. PMID: 8485146

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

Berry93: Berry A, Marshall KE (1993). "Identification of zinc-binding ligands in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli." FEBS Lett 318(1);11-6. PMID: 8436219

Blom96: Blom NS, Tetreault S, Coulombe R, Sygusch J (1996). "Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase." Nat Struct Biol 3(10);856-62. PMID: 8836102

Bock66: Bock A, Neidhardt FC (1966). "Properties of a Mutant of Escherichia coli with a Temperature-sensitive Fructose-1,6-Diphosphate Aldolase." J Bacteriol 92(2);470-6. PMID: 16562137

Bock66a: Bock A, Neidhardt FC (1966). "Isolation of a Mutant of Escherichia coli with a Temperature-sensitive Fructose-1,6-Diphosphate Aldolase Activity." J Bacteriol 92(2);464-469. PMID: 16562136

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

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."

Hall99a: 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

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

Irani77: Irani MH, Maitra PK (1977). "Properties of Escherichia coli mutants deficient in enzymes of glycolysis." J Bacteriol 132(2);398-410. PMID: 410789

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

Katayama02: Katayama A, Tsujii A, Wada A, Nishino T, Ishihama A (2002). "Systematic search for zinc-binding proteins in Escherichia coli." Eur J Biochem 269(9);2403-13. PMID: 11985624

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

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

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

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

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

Ruffler73: Ruffler D, Bock A (1973). "Location of the structural gene for fructose-1,6-diphosphate aldolase in Escherichia coli." J Bacteriol 116(2);1054-5. PMID: 4583229

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

Schreyer73: Schreyer R, Bock A (1973). "Phenotypic suppression of a fructose-1,6-diphosphate aldolase mutation in Escherichia coli." J Bacteriol 115(1);268-76. PMID: 4577744

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

Su75: Su CH, Merlie JP, Goldfine H (1975). "Rapid cessation of phospholipid synthesis in fructose-1,6-diphosphate aldolase mutants of Escherichia coli." J Bacteriol 122(2);565-9. PMID: 1092657

Szwergold95: Szwergold BS, Ugurbil K, Brown TR (1995). "Properties of fructose-1,6-bisphosphate aldolase from Escherichia coli: an NMR analysis." Arch Biochem Biophys 317(1);244-52. PMID: 7872790

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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.

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 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."

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

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

Zhang11: Zhang Z, Tan M, Xie Z, Dai L, Chen Y, Zhao Y (2011). "Identification of lysine succinylation as a new post-translational modification." Nat Chem Biol 7(1);58-63. PMID: 21151122

Other References Related to Gene Regulation

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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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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