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Escherichia coli K-12 substr. MG1655 Pathway: L-arginine degradation III (arginine decarboxylase/agmatinase pathway)
Inferred from experiment

Pathway diagram: L-arginine degradation III (arginine decarboxylase/agmatinase pathway)

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Schematic showing all replicons, marked with selected genes

Genetic Regulation Schematic

Genetic regulation schematic for L-arginine degradation III (arginine decarboxylase/agmatinase pathway)

Superclasses: BiosynthesisAmines and Polyamines Biosynthesis
Degradation/Utilization/AssimilationAmino Acids DegradationProteinogenic Amino Acids DegradationL-arginine Degradation

This arginine catabolic pathway has been discovered in Escherichia coli K-12 by Shaibe et al. [Shaibe85]. The pathway is essentially identical to an anabolic pathway that is used by many bacteria for the biosynthesis of putrescine (see putrescine biosynthesis I [Morris70]. Even though the main catabolic arginine pathway of Escherichia coli K-12 is the succinyltransferase pathway ( L-arginine degradation II (AST pathway)), this pathway provides an alternative route, and is used under certain growth conditions. Interestingly, unlike Escherichia coli K-12, wild-type E. coli strains are unable to use L-arginine as a carbon source, even though they can use it as a nitrogen source [Cunin86].

Escherichia coli K-12 has two forms of the enzyme arginine decarboxylase: a constitutive biosynthetic form, encoded by the speA gene, and an inducible catabolic form, encoded by the adiA gene. When the catabolic form is not expressed, the pathway operates only in an anabolic manner, catalyzing the biosynthesis of putrescine, which is used by the bacteria either directly or as a precursor for the biosynthesis of other polyamines (see superpathway of polyamine biosynthesis I). However, when the cells are grown in an arginine-rich medium, especially if the medium is acidic and conditions are semi-anaerobic, the catabolic arginine decarboxylase is expressed, and the pathway operates in a catabolic manner, feeding putrescine via 4-aminobutanoate and succinate into the TCA cycle I (prokaryotic) [Tabor85].

Superpathways: superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation, superpathway of L-arginine and L-ornithine degradation

Variants: L-arginine degradation II (AST pathway)

Created 06-Jan-2004 by Arnaud M, SRI International
Revised 14-Oct-2005 by Caspi R, SRI International


Cunin86: Cunin R, Glansdorff N, Pierard A, Stalon V (1986). "Biosynthesis and metabolism of arginine in bacteria." Microbiol Rev 1986;50(3);314-52. PMID: 3534538

Morris70: Morris DR, Jorstad CM (1970). "Isolation of conditionally putrescine-deficient mutants of Escherichia coli." J Bacteriol 101(3);731-7. PMID: 4908781

Shaibe85: Shaibe E, Metzer E, Halpern YS (1985). "Metabolic pathway for the utilization of L-arginine, L-ornithine, agmatine, and putrescine as nitrogen sources in Escherichia coli K-12." J Bacteriol 163(3);933-7. PMID: 3897201

Tabor85: Tabor CW, Tabor H (1985). "Polyamines in microorganisms." Microbiol Rev 1985;49(1);81-99. PMID: 3157043

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Andrell09: Andrell J, Hicks MG, Palmer T, Carpenter EP, Iwata S, Maher MJ (2009). "Crystal structure of the acid-induced arginine decarboxylase from Escherichia coli: reversible decamer assembly controls enzyme activity." Biochemistry 48(18);3915-27. PMID: 19298070

Bitonti87: Bitonti AJ, Casara PJ, McCann PP, Bey P (1987). "Catalytic irreversible inhibition of bacterial and plant arginine decarboxylase activities by novel substrate and product analogues." Biochem J 1987;242(1);69-74. PMID: 3297044

Blethen68: Blethen SL, Boeker EA, Snell EE (1968). "Argenine decarboxylase from Escherichia coli. I. Purification and specificity for substrates and coenzyme." J Biol Chem 1968;243(8);1671-7. PMID: 4870599

Boeker68: Boeker EA, Snell EE (1968). "Arginine decarboxylase from Escherichia coli. II. Dissociation and reassociation of subunits." J Biol Chem 243(8);1678-84. PMID: 4870600

Boyle84: Boyle SM, Markham GD, Hafner EW, Wright JM, Tabor H, Tabor CW (1984). "Expression of the cloned genes encoding the putrescine biosynthetic enzymes and methionine adenosyltransferase of Escherichia coli (speA, speB, speC and metK)." Gene 30(1-3);129-36. PMID: 6392022

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Buch85: Buch JK, Boyle SM (1985). "Biosynthetic arginine decarboxylase in Escherichia coli is synthesized as a precursor and located in the cell envelope." J Bacteriol 163(2);522-7. PMID: 3894328

Carvajal04: Carvajal N, Orellana MS, Salas M, Enriquez P, Alarcon R, Uribe E, Lopez V (2004). "Kinetic studies and site-directed mutagenesis of Escherichia coli agmatinase. A role for Glu274 in binding and correct positioning of the substrate guanidinium group." Arch Biochem Biophys 430(2);185-90. PMID: 15369817

Carvajal99: Carvajal N, Lopez V, Salas M, Uribe E, Herrera P, Cerpa J (1999). "Manganese is essential for catalytic activity of Escherichia coli agmatinase." Biochem Biophys Res Commun 258(3);808-11. PMID: 10329468

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

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

Giles07: Giles TN, Graham DE (2007). "Characterization of an acid-dependent arginine decarboxylase enzyme from Chlamydophila pneumoniae." J Bacteriol 189(20);7376-83. PMID: 17693492

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."

Gong03a: Gong S, Richard H, Foster JW (2003). "YjdE (AdiC) is the arginine:agmatine antiporter essential for arginine-dependent acid resistance in Escherichia coli." J Bacteriol 185(15);4402-9. PMID: 12867448

Hafner77: Hafner EW, Tabor CW, Tabor H (1977). "Isolation of a metK mutant with a temperature-sensitive S-adenosylmethionine synthetase." J Bacteriol 132(3);832-40. PMID: 336609

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by Pathway Tools version 19.5 (software by SRI International) on Wed May 4, 2016, biocyc13.