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Escherichia coli K-12 substr. MG1655 Enzyme: multifunctional 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase and oxaloacetate decarboxylase



Gene: eda Accession Numbers: EG10256 (EcoCyc), b1850, ECK1851

Synonyms: hga, kdgA, kga

Regulation Summary Diagram: ?

Subunit composition of multifunctional 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase and oxaloacetate decarboxylase = [Eda]3

Summary:
Eda: "Entner-Doudoroff aldolase"

Gene Citations: [Egan92]

Locations: cytosol, membrane

Map Position: [1,930,139 <- 1,930,780] (41.6 centisomes)
Length: 642 bp / 213 aa

Molecular Weight of Polypeptide: 22.284 kD (from nucleotide sequence)

pI: 5.83, 5.89 [VanBogelen92]

Unification Links: ASAP:ABE-0006164 , CGSC:826 , DIP:DIP-36196N , EchoBASE:EB0252 , EcoGene:EG10256 , EcoliWiki:b1850 , ModBase:P0A955 , OU-Microarray:b1850 , PortEco:eda , PR:PRO_000022502 , Pride:P0A955 , Protein Model Portal:P0A955 , RefSeq:NP_416364 , RegulonDB:EG10256 , SMR:P0A955 , String:511145.b1850 , UniProt:P0A955

Relationship Links: InterPro:IN-FAMILY:IPR000887 , InterPro:IN-FAMILY:IPR013785 , PDB:Structure:1EUA , PDB:Structure:1EUN , PDB:Structure:1FQ0 , PDB:Structure:1FWR , PDB:Structure:1WAU , PDB:Structure:1WBH , PDB:Structure:2C0A , Pfam:IN-FAMILY:PF01081 , Prosite:IN-FAMILY:PS00159 , Prosite:IN-FAMILY:PS00160

In Paralogous Gene Group: 352 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008675 - 2-dehydro-3-deoxy-phosphogluconate aldolase activity Inferred from experiment Inferred by computational analysis [GOA01, Fradkin71]
GO:0008700 - 4-hydroxy-2-oxoglutarate aldolase activity Inferred from experiment Inferred by computational analysis [GOA01, Walters08]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Lasserre06]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism glyoxylate degradation
metabolism energy metabolism, carbon Entner-Doudoroff

Essentiality data for eda 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]

Enzymatic reaction of: oxaloacetate decarboxylase

Synonyms: oxaloacetate β-decarboxylase, oxaloacetate carboxy-lyase

EC Number: 4.1.1.3

oxaloacetate + H+ <=> pyruvate + CO2

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Summary:
The eda gene codes for a multifunctional enzyme. One activity, KDPG aldolase, is part of the Entner-Doudoroff pathway. The other, KHG aldolase participates in the regulation of intracellular levels of glyoxylate. The enzyme also has oxaloacetate decarboxylase activity and participates in the dissimilation of glyoxylate to pyruvate. [Patil92, Kornberg61]


Enzymatic reaction of: 2-keto-3-deoxygluconate 6-phosphate aldolase

Synonyms: 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase, P-2-keto-3-deoxy-gluconate aldolase, 2-dehydro-3-deoxyphosphogluconate aldolase, KDPG-aldolase, phospho-2-keto-3-deoxygluconate aldolase, phospho-2-dehydro-3-deoxygluconate aldolase, 2-keto-3-deoxy-6-phosphogluconate aldolase

EC Number: 4.1.2.14

2-dehydro-3-deoxy-D-gluconate 6-phosphate <=> D-glyceraldehyde 3-phosphate + pyruvate

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

The reaction is favored in the direction shown.

In Pathways: superpathway of glycolysis and Entner-Doudoroff , superpathway of hexuronide and hexuronate degradation , superpathway of β-D-glucuronide and D-glucuronate degradation , Entner-Doudoroff pathway I , D-fructuronate degradation

Summary:
The gene eda codes for a trimeric multifunctional enzyme. The enzyme 2-dehydro-3-deoxyphosphogluconate aldolase catalyzes an aldol cleavage reaction in the Entner-Doudoroff pathway. The enzyme 4-hydroxy-2-oxoglutarate aldolase cleaves 2-keto-4-hydroxyglutarate and participates in the regulation of the intracellular level of glyoxylate. The aldolase can also catalyze the β-decarboxylation of oxalacetate. [Patil92, Egan92]

Inhibitors (Competitive): D-gluconate 6-phosphate [Pouyssegur71a] , D-glyceraldehyde 3-phosphate


Enzymatic reaction of: 2-keto-4-hydroxyglutarate aldolase

Synonyms: 4-hydroxy-2-oxoglutarate glyoxylate-lyase, KHG-aldolase, 2-oxo-4-hydroxyglutarate aldolase, 4-hydroxy-2-oxoglutarate aldolase

EC Number: 4.1.3.42

(4S)-4-hydroxy-2-oxoglutarate <=> glyoxylate + pyruvate

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.

Alternative Substrates for (4S)-4-hydroxy-2-oxoglutarate: 2-keto-4-hydroxybutyrate , oxaloacetate

Summary:
The gene eda codes for a trimeric multifunctional enzyme. The enzyme 2-dehydro-3-deoxyphosphogluconate aldolase catalyzes an aldol cleavage reaction in the Entner-Doudoroff pathway. The enzyme 4-hydroxy-2-oxoglutarate aldolase participates in the regulation of the intracellular level of glyoxylate. The aldolase can also catalyze the β-decarboxylation of oxalacetate. [Vlahos88, Patil92, Egan92] The E. coli KHG aldolase is stereoselective for the L isomer of 2-keto-4-hydroxyglutarate. [Patil92, Nishihara72] It is a Schiff-base mechanism (class I type) aldolase. [Grady81]

Inhibitors (Competitive): acetaldehyde , citrate , hydroxypyruvate , (4R)-4-hydroxy-2-oxoglutarate [Comment 5] , glyoxylate [Grady81] , pyruvate

Inhibitors (Unknown Mechanism): 4-mercuriphenylsulfonate , iodoacetate , N-ethylmaleimide [Comment 6] , 3-bromopyruvate [Helmward89, Vlahos90]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 8 -> 9
[UniProt14]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 45
[Fullerton06, Walters08, UniProt14]
Alternate sequence: E → N; UniProt: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity.
Active-Site 45
[Vlahos88, Vlahos90, UniProt11]
.
Amino-Acid-Sites-That-Bind 49
[UniProt14]
UniProt: Substrate.
Active-Site 49
[Vlahos88, Vlahos90, UniProt11]
.
Amino-Acid-Sites-That-Bind 73
[UniProt14]
UniProt: Substrate.
Mutagenesis-Variant 133
[Wymer01, UniProt14]
Alternate sequence: K → Q; UniProt: Absence of aldolase activity. Shows a markedly altered substrate specificity relative to the wild-type, with an enhanced activity against pyridine carboxaldehyde, benzaldehyde, and alpha- ketobutyrate; when associated with k-161.
Amino-Acid-Sites-That-Bind 133
[UniProt14]
UniProt: Substrate (covalent).
Active-Site 133
[Vlahos88, Vlahos90, UniProt11]
UniProt: Schiff-base intermediate with KHG or pyruvate.
Mutagenesis-Variant 161
[Wymer01, Walters08, UniProt14]
Alternate sequence: T → V; UniProt: Little stereoselectivity, accepting KDPG and KDPGal as substrate with roughly equal efficacy. It strongly diminishes the activity against KDPG and slightly increases activity against KDPGal.
Alternate sequence: T → K; UniProt: Shows activity significantly greater than wild-type. Shows a markedly altered substrate specificity relative to the wild-type, with an enhanced activity against pyridine carboxaldehyde, benzaldehyde, and alpha-ketobutyrate; when associated with Q-133.
Amino-Acid-Sites-That-Bind 161
[UniProt14]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 163
[UniProt14]
UniProt: Substrate; via amide nitrogen.
Mutagenesis-Variant 168
[Wymer01, UniProt14]
Alternate sequence: N → S; UniProt: Shows activity significantly greater than wild-type.
Amino-Acid-Sites-That-Bind 184
[UniProt14]
UniProt: Substrate.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1850 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10256; 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

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

Egan92: Egan SE, Fliege R, Tong S, Shibata A, Wolf RE, Conway T (1992). "Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon." J Bacteriol 1992;174(14);4638-46. PMID: 1624451

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

Fradkin71: Fradkin JE, Fraenkel DG (1971). "2-keto-3-deoxygluconate 6-phosphate aldolase mutants of Escherichia coli." J Bacteriol 108(3);1277-83. PMID: 4945194

Fullerton06: Fullerton SW, Griffiths JS, Merkel AB, Cheriyan M, Wymer NJ, Hutchins MJ, Fierke CA, Toone EJ, Naismith JH (2006). "Mechanism of the Class I KDPG aldolase." Bioorg Med Chem 14(9);3002-10. PMID: 16403639

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."

Grady81: Grady SR, Wang JK, Dekker EE "Steady-state kinetics and inhibition studies of the aldol condensation reaction catalyzed by bovine liver and Escherichia coli 2-keto-4-hydroxyglutarate aldolase." Biochemistry 1981;20:2497-2502.

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

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

Kornberg61: Kornberg HL, Sadler JR "Metabolism of C2 compounds in micro-organisms." BiochemJ 1961;81:503-513.

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

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

Nishihara72: Nishihara H, Dekker EE "Purification, substrate specificity and binding, beta-decarboxylase activity, and other properties of Escherichia coli 2-keto-4-hydroxyglutarate aldolase." J Biol Chem 1972;247:5079-5087.

Patil92: Patil RV, Dekker EE (1992). "Cloning, nucleotide sequence, overexpression, and inactivation of the Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene." J Bacteriol 1992;174(1);102-7. PMID: 1339418

Pouyssegur71a: Pouyssegur JM, Stoeber FR (1971). "[The common degradative pathway for hexuronates in Escherichia coli K 12. Purification, properties and individuality of 2-keto-3-deoxy-6-phospho-D-gluconate aldolase]." Eur J Biochem 1971;21(3);363-73. PMID: 4936448

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." 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."

VanBogelen92: VanBogelen RA, Sankar P, Clark RL, Bogan JA, Neidhardt FC (1992). "The gene-protein database of Escherichia coli: edition 5." Electrophoresis 1992;13(12);1014-54. PMID: 1286664

Vlahos88: Vlahos CJ, Dekker EE (1988). "The complete amino acid sequence and identification of the active-site arginine peptide of Escherichia coli 2-keto-4-hydroxyglutarate aldolase." J Biol Chem 1988;263(24);11683-91. PMID: 3136164

Vlahos90: Vlahos CJ, Dekker EE (1990). "Active-site residues of 2-keto-4-hydroxyglutarate aldolase from Escherichia coli. Bromopyruvate inactivation and labeling of glutamate 45." J Biol Chem 1990;265(33);20384-9. PMID: 1978721

Walters08: Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ (2008). "Characterization and crystal structure of Escherichia coli KDPGal aldolase." Bioorg Med Chem 16(2):710-20. PMID: 17981470

Wymer01: Wymer N, Buchanan LV, Henderson D, Mehta N, Botting CH, Pocivavsek L, Fierke CA, Toone EJ, Naismith JH (2001). "Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli." Structure 9(1);1-9. PMID: 11342129

Other References Related to Gene Regulation

Kaleta10: Kaleta C, Gohler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S (2010). "Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis." BMC Syst Biol 4;116. PMID: 20718955

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Murray05: Murray EL, Conway T (2005). "Multiple regulators control expression of the Entner-Doudoroff aldolase (Eda) of Escherichia coli." J Bacteriol 187(3);991-1000. PMID: 15659677

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

Rodionov00: Rodionov DA, Mironov AA, Rakhmaninova AB, Gelfand MS (2000). "Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria." Mol Microbiol 38(4);673-83. PMID: 11115104


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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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