Escherichia coli K-12 substr. MG1655 Enzyme: D-amino acid dehydrogenase

Gene: dadA Accession Numbers: EG11407 (EcoCyc), b1189, ECK1177

Synonyms: dadR

Regulation Summary Diagram: ?

Regulation summary diagram for dadA

Subunit composition of D-amino acid dehydrogenase = [DadA]2
         D-amino acid dehydrogenase = DadA

E. coli can utilize L- and D-alanine as the sole source of carbon, nitrogen and energy [Franklin76]. D-amino acid dehydrogenase is the second enzyme of the L-alanine degradation I pathway. The enzyme has broad substrate specificity; it catalyzes the oxidative deamination of many D-amino acids, although D-alanine is the best substrate [Franklin76, Wild81]. The enzyme is membrane-associated and linked to the respiratory chain [Jones83, Franklin76].

Regulatory mutations (dadR) increasing expression of DadA (and thus, likely the expression of the dadAX operon, which also encodes D-alanine racemase) lead to the ability to utizile D-isomers of several amino acids [Kuhn71]. Both L-alanine and D-alanine induce the expression of dadA, and expression is catabolite-repressible [Wild81, Wild82].

dadA mutants lack the ability to utilize either L-alanine or D-alanine as the sole source of carbon [Beelen73, Wild81].

In the final step of a partial purification of the enzyme from E. coli K-12, the enzyme eluted in a single peak of ~100 kDa [Jones83a]. Purification of D-amino acid dehydrogenase from E. coli B showed two subunits of apparently different sizes, a 45 kDa subunit that may be encoded by dadA, and a 55 kDa subunit for which no gene had been identified [Olsiewski80]. As this is the only report of two non-identical subunits, and the enzyme was purified from E. coli B, D-amino acid dehydrogenase is here represented as a dimer of identical DadA subunits.

DadA: "D-amino acid dehydrogenase" [Wild81]

Citations: [Franklin81]

Gene Citations: [Wild85, Lobocka94]

Locations: inner membrane

Map Position: [1,236,794 -> 1,238,092] (26.66 centisomes, 96°)
Length: 1299 bp / 432 aa

Molecular Weight of Polypeptide: 47.607 kD (from nucleotide sequence), 45.0 kD (experimental) [Olsiewski80 ]

Molecular Weight of Multimer: 100.0 kD (experimental) [Jones83a]

Unification Links: ASAP:ABE-0003995 , CGSC:884 , CGSC:18433 , DIP:DIP-6852N , EchoBASE:EB1379 , EcoGene:EG11407 , EcoliWiki:b1189 , ModBase:P0A6J5 , OU-Microarray:b1189 , PortEco:dadA , PR:PRO_000022396 , Pride:P0A6J5 , Protein Model Portal:P0A6J5 , RefSeq:NP_415707 , RegulonDB:EG11407 , SMR:P0A6J5 , String:511145.b1189 , UniProt:P0A6J5

Relationship Links: InterPro:IN-FAMILY:IPR006076 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR023080 , Pfam:IN-FAMILY:PF01266

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for dadA

GO Terms:

Biological Process: GO:0019480 - L-alanine oxidation to pyruvate via D-alanine Inferred from experiment [Wild81, Beelen73]
GO:0055130 - D-alanine catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Wild81]
GO:0019478 - D-amino acid catabolic process Inferred by computational analysis [GOA06, GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008718 - D-amino-acid dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Franklin76, Jones83]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, Jones83a, Franklin76]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: metabolism carbon utilization amino acids

Essentiality data for dadA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Last-Curated ? 20-Apr-2011 by Keseler I , SRI International

Enzymatic reaction of: D-amino-acid:quinone oxidoreductase (deaminating) (D-amino acid dehydrogenase)

EC Number:

Transport reaction diagram for D-amino-acid:quinone oxidoreductase (deaminating)

Alternative Substrates for a D-amino acid: D-alanine [Franklin76 , Wild81 ] , D-phenylalanine [Franklin76 , Wild81 ] , D-methionine [Franklin76 , Wild81 ] , D-asparagine [Franklin76 , Wild81 ] , D-leucine [Wild81 ]

The substrate range of the native (membrane-associated) and solubilized enzyme has been investigated [Wild81, Jones83, Franklin76]. The solubilized enzyme has a pH optimum of 7.9 [Jones83].

Cofactors or Prosthetic Groups: FAD

Kinetic Parameters:

Km (μM)

pH(opt): 8.9 [Jones83]

Enzymatic reaction of: D-alanine:quinone oxidoreductase (deaminating) (D-amino acid dehydrogenase)

EC Number: 1.4.5.-

Transport reaction diagram for D-alanine:quinone oxidoreductase (deaminating)

In Pathways: L-alanine degradation I

Purification of the enzyme was first reported from E. coli B [Olsiewski80].

The solubilized enzyme has a pH optimum of 7.9 [Jones83].

Cofactors or Prosthetic Groups: FAD

Kinetic Parameters:

Km (μM)

pH(opt): 8.9 [Jones83]

Sequence Features

Protein sequence of D-amino acid dehydrogenase with features indicated

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 3 -> 17
UniProt: FAD; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1189 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11407; confirmed by SwissProt match.


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

Beelen73: Beelen RH, Feldmann AM, Wijsman HJ (1973). "A regulatory gene and a structural gene for alaninase in Escherichia coli." Mol Gen Genet 121(4);369-74. PMID: 4571807

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

Franklin76: Franklin FC, Venables WA (1976). "Biochemical, genetic, and regulatory studies of alanine catabolism in Escherichia coli K12." Mol Gen Genet 149(2);229-37. PMID: 13292

Franklin81: Franklin FC, Venables WA, Wijsman HJ (1981). "Genetic studies of D-alanine-dehydrogenase-less mutants of Escherichia coli K12." Genet Res 1981;38(2);197-208. PMID: 7035293

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Jones83: Jones H, Venables WA (1983). "Effects of solubilisation on some properties of the membrane-bound respiratory enzyme D-amino acid dehydrogenase of Escherichia coli." FEBS Lett 151(2);189-92. PMID: 6131836

Jones83a: Jones H, Venables WA (1983). "Solubilisation of D-amino acid dehydrogenase of Escherichia coli K12 and its re-binding to envelope preparations." Biochimie 65(3);177-83. PMID: 6133564

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

Kuhn71: Kuhn J, Somerville RL (1971). "Mutant strains of Escherichia coli K12 that use D-amino acids." Proc Natl Acad Sci U S A 68(10);2484-7. PMID: 4400212

Lobocka94: Lobocka M, Hennig J, Wild J, Klopotowski T (1994). "Organization and expression of the Escherichia coli K-12 dad operon encoding the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase." J Bacteriol 1994;176(5);1500-10. PMID: 7906689

Olsiewski80: Olsiewski PJ, Kaczorowski GJ, Walsh C (1980). "Purification and properties of D-amino acid dehydrogenase, an inducible membrane-bound iron-sulfur flavoenzyme from Escherichia coli B." J Biol Chem 1980;255(10);4487-94. PMID: 6102989

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Wild81: Wild J, Klopotowski T (1981). "D-Amino acid dehydrogenase of Escherichia coli K12: positive selection of mutants defective in enzyme activity and localization of the structural gene." Mol Gen Genet 181(3);373-8. PMID: 6113535

Wild82: Wild J, Obrepalska B (1982). "Regulation of expression of the dadA gene encoding D-amino acid dehydrogenase in Escherichia coli: analysis of dadA-lac fusions and direction of dadA transcription." Mol Gen Genet 1982;186(3);405-10. PMID: 6126797

Wild85: Wild J, Hennig J, Lobocka M, Walczak W, Klopotowski T (1985). "Identification of the dadX gene coding for the predominant isozyme of alanine racemase in Escherichia coli K12." Mol Gen Genet 1985;198(2);315-22. PMID: 3920477

Other References Related to Gene Regulation

Mathew96: Mathew E, Zhi J, Freundlich M (1996). "Lrp is a direct repressor of the dad operon in Escherichia coli." J Bacteriol 1996;178(24);7234-40. PMID: 8955407

Zhi98: Zhi J, Mathew E, Freundlich M (1998). "In vitro and in vivo characterization of three major dadAX promoters in Escherichia coli that are regulated by cyclic AMP-CRP and Lrp." Mol Gen Genet 1998;258(4);442-7. PMID: 9648752

Zhi99: Zhi J, Mathew E, Freundlich M (1999). "Lrp binds to two regions in the dadAX promoter region of Escherichia coli to repress and activate transcription directly." Mol Microbiol 1999;32(1);29-40. PMID: 10216857

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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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