Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: aldehyde dehydrogenase A, NAD-linked



Gene: aldA Accession Numbers: EG10035 (EcoCyc), b1415, ECK1408

Synonyms: ald

Regulation Summary Diagram: ?

Subunit composition of aldehyde dehydrogenase A, NAD-linked = [AldA]4

Summary:
Aldehyde dehydrogenase A is an enzyme of relatively broad substrate specificity for small α-hydroxyaldehyde substrates. It is thus utilized in several metabolic pathways [Baldoma87].

L-fucose and L-rhamnose are metabolized through parallel pathways which converge after their corresponding aldolase reactions yielding the same products: dihydoxy-acetone phosphate and L-lactaldehyde. Aerobically, aldehyde dehydrogenase A oxidizes L-lactaldehyde to L-lactate [Chen87a, Baldoma87].

In parallel pathways utilizing the same enzymes, D-arabinose and L-lyxose can be metabolized to dihydoxy-acetone phosphate and glycolaldehyde, which is oxidized to glycolate by aldehyde dehydrogenase A [LeBlanc71, Badia91].

Crystal structures of the enzyme alone and in ternary and binary complexes have been solved [Di07].

Aldehyde dehydrogenase A is only present under aerobic conditions and is most highly induced by the presence of fucose, rhamnose or glutamate [Hacking76, Baldoma87, Baldoma88]. The enzyme is inhibited by NADH, which may act as a switch to shift from oxidation of lactaldehyde to its reduction by propanediol oxidoreductase [Baldoma88]. AldA is upregulated during short-term adaptation to glucose limitation [Wick01, Franchini06].

Based on sequence similarity, AldA was predicted to be a succinate-semialdehyde dehydrogenase [Reed03].

Regulation of aldA expression has been investigated. The gene is regulated by catabolite repression [Quintilla91, Limon97, Eppler02], repression under anaerobic conditions via ArcA [Limon97, Pellicer99], and induction by the carbon source [Pellicer99].

An aldA mutant shows slower growth on fucose and rhamnose than wild type [Chen87a].

AldA: "lactaldehyde dehydrogenase"

Gene Citations: [Pellicer99a]

Locations: cytosol

Map Position: [1,486,256 -> 1,487,695] (32.03 centisomes)
Length: 1440 bp / 479 aa

Molecular Weight of Polypeptide: 52.273 kD (from nucleotide sequence), 55.0 kD (experimental) [Baldoma87 ]

Molecular Weight of Multimer: 220.0 kD (experimental) [Baldoma87]

pI: 5.24

Isozyme Sequence Similarity:
AldB: YES

Unification Links: ASAP:ABE-0004725 , CGSC:17767 , DIP:DIP-9081N , EchoBASE:EB0034 , EcoGene:EG10035 , EcoliWiki:b1415 , Mint:MINT-1313045 , ModBase:P25553 , OU-Microarray:b1415 , PortEco:aldA , PR:PRO_000022075 , Pride:P25553 , Protein Model Portal:P25553 , RefSeq:NP_415933 , RegulonDB:EG10035 , SMR:P25553 , String:511145.b1415 , UniProt:P25553

Relationship Links: InterPro:IN-FAMILY:IPR015590 , InterPro:IN-FAMILY:IPR016160 , InterPro:IN-FAMILY:IPR016161 , InterPro:IN-FAMILY:IPR016162 , InterPro:IN-FAMILY:IPR016163 , PDB:Structure:2HG2 , PDB:Structure:2ILU , PDB:Structure:2IMP , PDB:Structure:2OPX , Pfam:IN-FAMILY:PF00171 , Prosite:IN-FAMILY:PS00070 , Prosite:IN-FAMILY:PS00687

In Paralogous Gene Group: 95 (14 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0019301 - rhamnose catabolic process Inferred from experiment [Chen87a]
GO:0042355 - L-fucose catabolic process Inferred from experiment [Hacking76]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008911 - lactaldehyde dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA01, Sridhara69, Baldoma87]
GO:0050569 - glycolaldehyde dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA01, Baldoma87]
GO:0004777 - succinate-semialdehyde dehydrogenase (NAD+) activity Inferred by computational analysis [Reed03]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism methylglyoxal metabolism

Essentiality data for aldA 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 ? 01-Nov-2007 by Keseler I , SRI International


Enzymatic reaction of: glycolaldehyde dehydrogenase (aldehyde dehydrogenase A, NAD-linked)

Synonyms: glycolaldehyde:NAD+ oxidoreductase

EC Number: 1.2.1.21

glycolaldehyde + NAD+ + H2O <=> glycolate + NADH + 2 H+

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 irreversible in the direction shown.

Alternative Substrates for glycolaldehyde: (S)-lactaldehyde [Caballero83 ]

In Pathways: superpathway of glycol metabolism and degradation , ethylene glycol degradation , D-arabinose degradation I

Summary:
Kinetic data was also measured by [RodriguezZavala06].

Cofactor Binding Comment: The enzyme was able to utilize NADP as a coenzyme under experimental conditions, but its activity was about 10 times lower than the NAD-dependent activity. [Boronat83]

Inhibitors (Unknown Mechanism): Zn2+ [Baldoma87] , glycolaldehyde [Baldoma87]

Kinetic Parameters:

Substrate
Km (μM)
Citations
glycolaldehyde
380.0
[Baldoma87]
NAD+
280.0
[Baldoma87]


Enzymatic reaction of: lactaldehyde dehydrogenase (aldehyde dehydrogenase A, NAD-linked)

Synonyms: (S)-lactaldehyde:NAD+ oxidoreductase

EC Number: 1.2.1.22

(S)-lactaldehyde + NAD+ + H2O <=> (S)-lactate + NADH + 2 H+

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 irreversible in the direction shown.

Alternative Substrates for (S)-lactaldehyde: L-glyceraldehyde [Zhu87 ] , glycolaldehyde [Caballero83 ]

In Pathways: superpathway of fucose and rhamnose degradation , methylglyoxal degradation IV , superpathway of methylglyoxal degradation , L-lactaldehyde degradation (aerobic)

Activators (Unknown Mechanism): a sulfhydryl group [Sridhara69]

Inhibitors (Unknown Mechanism): NADH [Baldoma88] , (S)-lactaldehyde [Baldoma87] , Cu2+ [Sridhara69, Baldoma87] , iodoacetate [Sridhara69]

Primary Physiological Regulators of Enzyme Activity: NADH

Kinetic Parameters:

Substrate
Km (μM)
Citations
NAD+
120.0
[Baldoma87]
(S)-lactaldehyde
40.0
[Baldoma87]

pH(opt): 10.5-11 [Sridhara69]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Link97, Hidalgo91]
 
Chain 2 -> 479
[UniProt09]
UniProt: Lactaldehyde dehydrogenase;
Nucleotide-Phosphate-Binding-Region 207 -> 213
[UniProt10a]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Active-Site 251
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;
Active-Site 285
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1415 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10035; 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

Badia91: Badia J, Gimenez R, Baldoma L, Barnes E, Fessner WD, Aguilar J (1991). "L-lyxose metabolism employs the L-rhamnose pathway in mutant cells of Escherichia coli adapted to grow on L-lyxose." J Bacteriol 1991;173(16);5144-50. PMID: 1650346

Baldoma87: Baldoma L, Aguilar J (1987). "Involvement of lactaldehyde dehydrogenase in several metabolic pathways of Escherichia coli K12." J Biol Chem 262(29);13991-6. PMID: 3308886

Baldoma88: Baldoma L, Aguilar J (1988). "Metabolism of L-fucose and L-rhamnose in Escherichia coli: aerobic-anaerobic regulation of L-lactaldehyde dissimilation." J Bacteriol 170(1);416-21. PMID: 3275622

Boronat83: Boronat A, Caballero E, Aguilar J (1983). "Experimental evolution of a metabolic pathway for ethylene glycol utilization by Escherichia coli." J Bacteriol 1983;153(1);134-9. PMID: 6336729

Caballero83: Caballero E, Baldoma L, Ros J, Boronat A, Aguilar J (1983). "Identification of lactaldehyde dehydrogenase and glycolaldehyde dehydrogenase as functions of the same protein in Escherichia coli." J Biol Chem 1983;258(12);7788-92. PMID: 6345530

Chen87a: Chen YM, Zhu Y, Lin EC (1987). "NAD-linked aldehyde dehydrogenase for aerobic utilization of L-fucose and L-rhamnose by Escherichia coli." J Bacteriol 1987;169(7);3289-94. PMID: 3298215

Di07: Di Costanzo L, Gomez GA, Christianson DW (2007). "Crystal structure of lactaldehyde dehydrogenase from Escherichia coli and inferences regarding substrate and cofactor specificity." J Mol Biol 366(2);481-93. PMID: 17173928

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

Eppler02: Eppler T, Postma P, Schutz A, Volker U, Boos W (2002). "Glycerol-3-phosphate-induced catabolite repression in Escherichia coli." J Bacteriol 184(11);3044-52. PMID: 12003946

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

Franchini06: Franchini AG, Egli T (2006). "Global gene expression in Escherichia coli K-12 during short-term and long-term adaptation to glucose-limited continuous culture conditions." Microbiology 152(Pt 7);2111-27. PMID: 16804185

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."

Hacking76: Hacking AJ, Lin EC (1976). "Disruption of the fucose pathway as a consequence of genetic adaptation to propanediol as a carbon source in Escherichia coli." J Bacteriol 126(3);1166-72. PMID: 181364

Hidalgo91: Hidalgo E, Chen YM, Lin EC, Aguilar J (1991). "Molecular cloning and DNA sequencing of the Escherichia coli K-12 ald gene encoding aldehyde dehydrogenase." J Bacteriol 1991;173(19);6118-23. PMID: 1917845

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

LeBlanc71: LeBlanc DJ, Mortlock RP (1971). "Metabolism of D-arabinose: a new pathway in Escherichia coli." J Bacteriol 106(1);90-6. PMID: 4928018

Limon97: Limon A, Hidalgo E, Aguilar J (1997). "The aldA gene of Escherichia coli is under the control of at least three transcriptional regulators." Microbiology 143 ( Pt 6);2085-95. PMID: 9202484

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

Pellicer99: Pellicer MT, Lynch AS, De Wulf P, Boyd D, Aguilar J, Lin EC (1999). "A mutational study of the ArcA-P binding sequences in the aldA promoter of Escherichia coli." Mol Gen Genet 261(1);170-6. PMID: 10071223

Pellicer99a: Pellicer MT, Fernandez C, Badia J, Aguilar J, Lin EC, Baldom L (1999). "Cross-induction of glc and ace operons of Escherichia coli attributable to pathway intersection. Characterization of the glc promoter." J Biol Chem 274(3);1745-52. PMID: 9880556

Quintilla91: Quintilla FX, Baldoma L, Badia J, Aguilar J (1991). "Aldehyde dehydrogenase induction by glutamate in Escherichia coli. Role of 2-oxoglutarate." Eur J Biochem 202(3);1321-5. PMID: 1684935

Reed03: Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)." Genome Biol 4(9);R54. PMID: 12952533

RodriguezZavala06: Rodriguez-Zavala JS, Allali-Hassani A, Weiner H (2006). "Characterization of E. coli tetrameric aldehyde dehydrogenases with atypical properties compared to other aldehyde dehydrogenases." Protein Sci 15(6);1387-96. PMID: 16731973

Sridhara69: Sridhara S, Wu TT (1969). "Purification and properties of lactaldehyde dehydrogenase from Escherichia coli." J Biol Chem 1969;244(19);5233-8. PMID: 4310089

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Wick01: Wick LM, Quadroni M, Egli T (2001). "Short- and long-term changes in proteome composition and kinetic properties in a culture of Escherichia coli during transition from glucose-excess to glucose-limited growth conditions in continuous culture and vice versa." Environ Microbiol 3(9);588-99. PMID: 11683869

Zhu87: Zhu Y, Lin EC (1987). "Loss of aldehyde dehydrogenase in an Escherichia coli mutant selected for growth on the rare sugar L-galactose." J Bacteriol 169(2);785-9. PMID: 3542971

Other References Related to Gene Regulation

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Liu04: Liu X, De Wulf P (2004). "Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling." J Biol Chem 279(13);12588-97. PMID: 14711822

Ozaki01: Ozaki T, Kumaki Y, Kitagawa R, Ogawa T (2001). "Anomalous DnaA protein binding to the regulatory region of the Escherichia coli aldA gene." Microbiology 147(Pt 1);153-9. PMID: 11160809


Report Errors or Provide Feedback
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 Fri Dec 19, 2014, BIOCYC14A.