Escherichia coli K-12 substr. MG1655 Enzyme: 2,3-diaminopropionate ammonia-lyase

Gene: ygeX Accession Numbers: G7490 (EcoCyc), b2871, ECK2867

Regulation Summary Diagram: ?

Regulation summary diagram for ygeX

Subunit composition of 2,3-diaminopropionate ammonia-lyase = [YgeX]2
         2,3-diaminopropionate ammonia-lyase = YgeX

Unlike Salmonella typhimurium, E. coli only shows weak growth on 2,3-diaminopropionate as the sole source of carbon. This difference may be due to the very low expression levels of 2,3-diaminopropionate ammonia-lyase in E. coli [Kalyani12].

2,3-Diaminopropionate ammonia-lyase is not stereospecific and catalyzes the α,β-elimination of both the D and L stereoisomer of 2,3-diaminopropionate [Uo02, Khan03]. The enzyme also exhibits weak activity toward D-serine, and does not exhibit activity toward L-serine, D-β-Cl-alanine, or L-β-Cl-alanine [Uo02].

The enzyme is homodimeric and contains a pyridoxal 5'-phosphate prosthetic group [Uo02, Khan03], belonging to the fold-type II family of PLP-containing enzymes [Uo02]. Crystal structures of the apo- and holoenzyme and the enzyme in complex with a reaction intermediate and substrate have been solved [Rajaram03, Bisht12]. Kinetic properties of mutants in active site residues were analyzed, and a reaction mechanism was proposed [Bisht12].

Locations: cytosol

Map Position: [3,005,532 -> 3,006,728] (64.78 centisomes, 233°)
Length: 1197 bp / 398 aa

Molecular Weight of Polypeptide: 43.328 kD (from nucleotide sequence), 43 kD (experimental) [Uo02 ]

Molecular Weight of Multimer: 78 kD (experimental) [Uo02]

Unification Links: ASAP:ABE-0009428 , EchoBASE:EB2866 , EcoGene:EG13054 , EcoliWiki:b2871 , ModBase:P66899 , OU-Microarray:b2871 , PortEco:ygeX , Pride:P66899 , Protein Model Portal:P66899 , RefSeq:NP_417347 , RegulonDB:G7490 , SMR:P66899 , String:511145.b2871 , UniProt:P66899

Relationship Links: InterPro:IN-FAMILY:IPR001926 , InterPro:IN-FAMILY:IPR010081 , InterPro:IN-FAMILY:IPR019871 , Panther:IN-FAMILY:PTHR10314:SF7 , PDB:Structure:4D9G , PDB:Structure:4D9I , PDB:Structure:4D9K , PDB:Structure:4D9M , PDB:Structure:4D9N , Pfam:IN-FAMILY:PF00291

In Paralogous Gene Group: 362 (8 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0009063 - cellular amino acid catabolic process Inferred by computational analysis [Uo02]
Molecular Function: GO:0008838 - diaminopropionate ammonia-lyase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Khan03, Uo02, Kalyani12]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA01a, Uo02]
GO:0042803 - protein homodimerization activity Inferred from experiment [Uo02]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [Gaudet10]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Essentiality data for ygeX 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]

Last-Curated ? 29-Aug-2012 by Keseler I , SRI International

Enzymatic reaction of: 2,3-diaminopropionate ammonia-lyase

Synonyms: diaminopropionatase, diaminopropionate ammonia-lyase, a,b-diaminopropionate ammonia-lyase, DAPAL

EC Number:

2,3-diaminopropanoate + H+ + H2O <=> 2 ammonium + pyruvate + 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 physiologically favored in the direction shown.

The Km for D-diaminopropionate is 100 µM, and the Km for L-diaminopropionate is 48 µM [Uo02].

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Khan03, Uo02]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)

pH(opt): 8 [Uo02]

Sequence Features

Protein sequence of 2,3-diaminopropionate ammonia-lyase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Active-Site 77
UniProt: Proton acceptor; for D-DAP ammonia-lyase activity.
Mutagenesis-Variant 77
[UniProt14, Bisht12, UniProt14]
K → H or R: No longer binds cofactor, loss of enzymatic activity.
N6-pyridoxal-phosphate-Lys-Modification 77
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: potential.
Active-Site 120
UniProt: Proton acceptor; for L-DAP ammonia-lyase activity.
Mutagenesis-Variant 120
[Bisht12, UniProt14]
UniProt: No activity on D-DAP, 150-fold reduced catalytic efficiency for L-DAP; alters substrate stereospecificity.
Mutagenesis-Variant 189
[Bisht12, UniProt14]
UniProt: 10000-fold reduced catalytic efficiency for both D- and L-DAP.
Disulfide-Bond-Site 265, 291
[Bisht12, UniProt14]

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Bisht12: Bisht S, Rajaram V, Bharath SR, Kalyani JN, Khan F, Rao AN, Savithri HS, Murthy MR (2012). "Crystal structure of Escherichia coli diaminopropionate ammonia-lyase reveals mechanism of enzyme activation and catalysis." J Biol Chem 287(24);20369-81. PMID: 22505717

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

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

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

Kalyani12: Kalyani JN, Ramachandra N, Kachroo AH, Mahadevan S, Savithri HS (2012). "Functional analysis of the genes encoding diaminopropionate ammonia lyase in Escherichia coli and Salmonella enterica serovar Typhimurium." J Bacteriol 194(20);5604-12. PMID: 22904288

Khan03: Khan F, Jala VR, Rao NA, Savithri HS (2003). "Characterization of recombinant diaminopropionate ammonia-lyase from Escherichia coli and Salmonella typhimurium." Biochem Biophys Res Commun 306(4);1083-8. PMID: 12821154

Rajaram03: Rajaram V, Rajaganapathi J, Khan F, Savithri HS, Murthy MR (2003). "Crystallization and preliminary X-ray diffraction studies on recombinant diaminopropionate ammonia lyase from Escherichia coli." Acta Crystallogr D Biol Crystallogr 59(Pt 9);1668-9. PMID: 12925808

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Uo02: Uo T, Yoshimura T, Nishiyama T, Esaki N (2002). "Gene cloning, purification, and characterization of 2,3-diaminopropionate ammonia-lyase from Escherichia coli." Biosci Biotechnol Biochem 66(12);2639-44. PMID: 12596860

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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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