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Escherichia coli K-12 substr. MG1655 Enzyme: cAMP phosphodiesterase



Gene: cpdA Accession Numbers: G7579 (EcoCyc), b3032, ECK3023

Synonyms: icc

Regulation Summary Diagram: ?

Summary:
cAMP phosphodiesterase hydrolyzes the important regulatory molecule cAMP and may thus influence the level of transcription of genes regulated by cAMP-CRP [Imamura96]. However, its rather low affinity for cAMP compared to the dissociation constant of cAMP from CRP suggests that the enzyme does not have a major impact on cAMP concentration in E. coli [Hantke11].

Usage of the unusual translation start codon UUG has been confirmed by amino-terminal sequencing of the purified protein and may be involved in translational regulation of CpdA expression [Imamura96]. CpdA belongs to a family of phosphodiesterases resembling purple acid phosphatases and other dimetallophosphoesterases [Richter02].

Expression of CpdA appears to be itself catabolite-repressed [Aboud71]. A cpdA mutant appears to have slightly increased intracellular levels of cAMP [Imamura96]. Overexpression of cpdA leads to increased resistance to hypochlorous acid stress due to derepression of rpoS [Barth09].

CpdA: "cyclic AMP phosphodiesterase" [Imamura96]

Locations: cytosol

Map Position: [3,174,028 <- 3,174,855] (68.41 centisomes)
Length: 828 bp / 275 aa

Molecular Weight of Polypeptide: 30.938 kD (from nucleotide sequence), 30.0 kD (experimental) [Nielsen73 ]

Unification Links: ASAP:ABE-0009957 , EchoBASE:EB2104 , EcoGene:EG12187 , EcoliWiki:b3032 , ModBase:P0AEW4 , OU-Microarray:b3032 , PortEco:cpdA , PR:PRO_000022988 , Pride:P0AEW4 , Protein Model Portal:P0AEW4 , RefSeq:NP_417504 , RegulonDB:G7579 , SMR:P0AEW4 , String:511145.b3032 , UniProt:P0AEW4

Relationship Links: InterPro:IN-FAMILY:IPR004843 , InterPro:IN-FAMILY:IPR013622 , InterPro:IN-FAMILY:IPR026575 , Pfam:IN-FAMILY:PF00149 , ProDom:IN-FAMILY:PD587589

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [Imamura96, UniProtGOA11a, GOA06, GOA01a, GOA01]
Molecular Function: GO:0004115 - 3',5'-cyclic-AMP phosphodiesterase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Imamura96]
GO:0008198 - ferrous iron binding Inferred from experiment [Nielsen73]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0004114 - 3',5'-cyclic-nucleotide phosphodiesterase activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA06]
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: regulation type of regulation posttranscriptional proteases, cleavage of compounds

Essentiality data for cpdA 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]

Credits:
Last-Curated ? 29-Dec-2010 by Keseler I , SRI International


Enzymatic reaction of: cAMP phosphodiesterase

Synonyms: cyclic AMP phosphodiesterase, cyclic 3',5'-adenosine monophosphate phosphodiesterase

EC Number: 3.1.4.53

cyclic-AMP + H2O <=> AMP + 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.

Summary:
cGMP is not a substrate [Nielsen73].

Cofactors or Prosthetic Groups: Fe2+ [Imamura96, Nielsen73]

Inhibitors (Unknown Mechanism): phosphate [Amin95]

Kinetic Parameters:

Substrate
Km (μM)
Citations
cyclic-AMP
500.0
[Imamura96]

pH(opt): 6.8-7 [Nielsen73]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 22
[UniProt11a]
UniProt: Metal cation 1; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 24
[UniProt11a]
UniProt: Metal cation 1; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 64
[UniProt11a]
UniProt: Metal cation 1; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 94
[UniProt11a]
UniProt: Metal cation 2; Non-Experimental Qualifier: by similarity.
Nucleotide-Phosphate-Binding-Region 94 -> 95
[UniProt11a]
UniProt: cAMP; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 164
[UniProt11a]
UniProt: Metal cation 2; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 203
[UniProt11a]
UniProt: Metal cation 2; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 205
[UniProt11a]
UniProt: Metal cation 1; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

Aboud71: Aboud M, Burger M (1971). "Cyclic 3';5' adenosine monophosphate-phosphodiesterase and the release of catabolite repression of beta-galactosidase by exogenous cyclic 3';5' adenosine monophosphate in Escherichia coli." Biochem Biophys Res Commun 43(1);174-82. PMID: 4325494

Amin95: Amin N, Peterkofsky A (1995). "A dual mechanism for regulating cAMP levels in Escherichia coli." J Biol Chem 270(20);11803-5. PMID: 7744829

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

Barth09: Barth E, Gora KV, Gebendorfer KM, Settele F, Jakob U, Winter J (2009). "Interplay of cellular cAMP levels, {sigma}S activity and oxidative stress resistance in Escherichia coli." Microbiology 155(Pt 5);1680-9. PMID: 19372151

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

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, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Hantke11: Hantke K, Winkler K, Schultz JE (2011). "Escherichia coli exports cyclic AMP via TolC." J Bacteriol 193(5);1086-9. PMID: 21183666

Imamura96: Imamura R, Yamanaka K, Ogura T, Hiraga S, Fujita N, Ishihama A, Niki H (1996). "Identification of the cpdA gene encoding cyclic 3',5'-adenosine monophosphate phosphodiesterase in Escherichia coli." J Biol Chem 1996;271(41);25423-9. PMID: 8810311

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

Nielsen73: Nielsen LD, Monard D, Rickenberg HV (1973). "Cyclic 3',5'-adenosine monophosphate phosphodiesterase of Escherichia coli." J Bacteriol 116(2);857-66. PMID: 4355491

Richter02: Richter W (2002). "3',5' Cyclic nucleotide phosphodiesterases class III: members, structure, and catalytic mechanism." Proteins 46(3);278-86. PMID: 11835503

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

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

Other References Related to Gene Regulation

Avison01: Avison MB, Horton RE, Walsh TR, Bennett PM (2001). "Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media." J Biol Chem 276(29);26955-61. PMID: 11350954


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, biocyc14.