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Escherichia coli K-12 substr. MG1655 Enzyme: cryptic adenine deaminase



Gene: adeD Accession Numbers: EG11692 (EcoCyc), b3665, ECK3656

Synonyms: adeC(B.s.), adu, yicP, ade

Regulation Summary Diagram: ?

Subunit composition of cryptic adenine deaminase = [AdeD]2
         cryptic adenine deaminase monomer = AdeD

Summary:
AdeD is a substrate-specific adenine deaminase [Matsui01]. In wild-type cells, levels of adenine deaminase are too low to satisfy the cellular purine requirement [Petersen02].

Two metal ions per subunit are required for optimal adenine deaminase activity [Kamat11b], and either Mn2+ or Fe2+ can satisfy this metal requirement [Kamat11]. The catalytically active Fe/Fe enzyme contains two high-spin ferrous iron ions. Site-directed mutagenesis of His92, His214, His235 and Glu185 result in loss of catalytic activity and metal binding, and certain mutations in His90 result in loss of metal binding [Kamat11b]. A reaction mechanism has been proposed [Kamat11b, Kamat11].

Ferrous iron-containing enzyme also has catalase activity; exposure to hydrogen peroxide eventually damages the enzyme by oxygenation of various amino acid residues, and its adenine deaminase activity is concurrently lost. Superoxide formation can also be measured [Kamat11].

AdeD expression appears to be induced by the presence of high amounts of adenine in the culture medium [Matsui01]. Transcription of ade can be activated by various promoter mutations and is repressed more than 10-fold by the H-NS protein in wild type [Petersen02].

Adu: [Kocharian82]

Ade: "adenine deaminase" [Petersen02]

Citations: [Shimaoka05]

Locations: cytosol

Map Position: [3,841,987 -> 3,843,753] (82.81 centisomes)
Length: 1767 bp / 588 aa

Molecular Weight of Polypeptide: 63.739 kD (from nucleotide sequence), 60 kD (experimental) [Matsui01 ]

Molecular Weight of Multimer: 120.0 kD (experimental) [Matsui01]

Unification Links: ASAP:ABE-0011979 , DIP:DIP-12439N , EchoBASE:EB1643 , EcoGene:EG11692 , EcoliWiki:b3665 , Mint:MINT-1285289 , ModBase:P31441 , OU-Microarray:b3665 , PortEco:ade , PR:PRO_000022055 , Pride:P31441 , Protein Model Portal:P31441 , RefSeq:NP_418121 , RegulonDB:EG11692 , SMR:P31441 , String:511145.b3665 , UniProt:P31441

Relationship Links: InterPro:IN-FAMILY:IPR006679 , InterPro:IN-FAMILY:IPR006680 , InterPro:IN-FAMILY:IPR011059 , InterPro:IN-FAMILY:IPR026912 , Pfam:IN-FAMILY:PF01979 , Pfam:IN-FAMILY:PF13382

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006146 - adenine catabolic process Inferred from experiment Inferred by computational analysis [GOA01a, Matsui01]
GO:0046101 - hypoxanthine biosynthetic process Inferred from experiment [Matsui01]
GO:0055114 - oxidation-reduction process Inferred from experiment [Kamat11]
Molecular Function: GO:0000034 - adenine deaminase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Matsui01]
GO:0004096 - catalase activity Inferred from experiment [Kamat11]
GO:0008198 - ferrous iron binding Inferred from experiment [Kamat11]
GO:0030145 - manganese ion binding Inferred from experiment [Matsui01]
GO:0042803 - protein homodimerization activity Inferred from experiment [Matsui01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Essentiality data for adeD 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 ? 04-Dec-2013 by Keseler I , SRI International


Enzymatic reaction of: adenine deaminase

Synonyms: adenine deaminase, adenine aminohydrolase, adenase, ADase, adenine aminase

EC Number: 3.5.4.2

adenine + H+ + H2O <=> ammonium + hypoxanthine

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:
If enzyme production is induced in medium containing an iron chelator, the purified enzyme shows ~100-fold higher kcat (200 s-1) and a lower KM of 400 µM for adenine [Kamat11b].

Either Mn2+ or Fe2+ can satisfy the metal requirement for the adenine deaminase activity [Kamat11].

Cofactors or Prosthetic Groups: Fe2+ [Kamat11], Mn2+ [Kamat11b, Matsui01]

Inhibitors (Unknown Mechanism): 6-chloropurine [Kamat11b]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
adenine
400.0
200.0
[Kamat11b]

T(opt): 60 °C [Matsui01]

pH(opt): 7-8 [Kamat11b]


Enzymatic reaction of: catalase (cryptic adenine deaminase)

EC Number: 1.11.1.6

2 hydrogen peroxide <=> 2 H2O + oxygen

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.

In Pathways: superoxide radicals degradation

Cofactors or Prosthetic Groups: Fe2+ [Kamat11]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
hydrogen peroxide
9000.0
200.0
[Kamat11]


Sequence Features

Feature Class Location Attached Group Citations
Metal-Binding-Site 90, 92, 214, 235 Mn2+
[Kamat11b]


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3665 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11692; 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

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

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

Kamat11: Kamat SS, Holmes-Hampton GP, Bagaria A, Kumaran D, Tichy SE, Gheyi T, Zheng X, Bain K, Groshong C, Emtage S, Sauder JM, Burley SK, Swaminathan S, Lindahl PA, Raushel FM (2011). "The catalase activity of diiron adenine deaminase." Protein Sci 20(12);2080-94. PMID: 21998098

Kamat11b: Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM (2011). "Catalytic mechanism and three-dimensional structure of adenine deaminase." Biochemistry 50(11);1917-27. PMID: 21247091

Kocharian82: Kocharian ShM, Kocharian AM, Meliksetian GO, Akopian ZhI (1982). "[Escherichia coli K-12 mutants assimilating adenine via a new metabolic pathway]." Genetika 18(6);906-15. PMID: 6809533

Matsui01: Matsui H, Shimaoka M, Kawasaki H, Takenaka Y, Kurahashi O (2001). "Adenine deaminase activity of the yicP gene product of Escherichia coli." Biosci Biotechnol Biochem 65(5);1112-8. PMID: 11440125

Petersen02: Petersen C, Moller LB, Valentin-Hansen P (2002). "The cryptic adenine deaminase gene of Escherichia coli. Silencing by the nucleoid-associated DNA-binding protein, H-NS, and activation by insertion elements." J Biol Chem 277(35);31373-80. PMID: 12077137

Shimaoka05: Shimaoka M, Kawasaki H, Takenaka Y, Kurahashi O, Matsui H (2005). "Effects of edd and pgi disruptions on inosine accumulation in Escherichia coli." Biosci Biotechnol Biochem 69(7);1248-55. PMID: 16041126

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


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 Sat Dec 20, 2014, biocyc11.