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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Pathway: arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)

Enzyme View:

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/Assimilation Amino Acids Degradation Arginine Degradation

Some taxa known to possess this pathway include ? : Aeromonas caviae , Pseudomonas aeruginosa

Expected Taxonomic Range: Proteobacteria

Summary:
This arginine catabolic pathway has been discovered in Pseudomonas aeruginosa by Mercenier et al [Mercenier80]. The pathway is essentially identical to an anabolic pathway that is used by higher plants, and many bacteria, for the biosynthesis of putrescine (see putrescine biosynthesis II [Smith64, Piotrowski03]. However, there are indications that in Pseudomonas aeruginosa the pathway also operates in a catabolic form, where the putrescine formed from arginine is degraded further to provide the bacteria with carbon and nitrogen. When grown on arginine as the sole carbon and nitrogen source, the activity of arginine decarboxylase increased significantly, and the addition of agmatine and N-carbamoylputrescine increased the synthesis of agmatine deiminase and N-carbamoylputrescine amidohydrolase. In addition, adding succinate, citrate, glutamine, or ammonia to the medium led to the repression of these enzymes, indicating that the pathway is regulated by both carbon catabolite repression as well as nitrogen catabolite repression [Mercenier80].

While there are several reports supporting the function of this pathway as a catabolic arginine degradation pathway [Haas84, Nakada01, Nakada03], it is clear that the main catabolic arginine pathway in Pseudomonads is the succinyltransferase pathway (see arginine degradation II (AST pathway)). In addition, unlike the case in Escherichia coli K-12, where there are two varieties of arginine decarboxylase, a biosynthetic variety and a degradative variety, there is no indication for the presence of a homolog of the degradative form in Pseudomonas aeruginosa. Thus, there is still some debate whether this is a true arginine degradation pathway. However, it is agreed that at least the last two steps of the pathway are used for catabolic agmatine degradation [Nakada03].

It should be noted that while this pathway has been studied mostly in Pseudomonas aeruginosa, it was also observed in Aeromonas caviae [Stalon82].

Variants: arginine degradation I (arginase pathway) , arginine degradation II (AST pathway) , arginine degradation III (arginine decarboxylase/agmatinase pathway) , arginine degradation V (arginine deiminase pathway) , arginine degradation VI (arginase 2 pathway) , arginine degradation VII (arginase 3 pathway) , arginine degradation VIII (arginine oxidase pathway) , arginine degradation IX (arginine:pyruvate transaminase pathway) , arginine degradation X (arginine monooxygenase pathway) , arginine degradation XI , arginine degradation XII , citrulline-nitric oxide cycle , D-arginine degradation , superpathway of arginine and ornithine degradation , superpathway of arginine, putrescine, and 4-aminobutyrate degradation

Credits:
Created 09-Jul-1998 by Ying HC , SRI International
Revised 10-Oct-2005 by Caspi R , SRI International


References

Haas84: Haas D, Matsumoto H, Moretti P, Stalon V, Mercenier A (1984). "Arginine degradation in Pseudomonas aeruginosa mutants blocked in two arginine catabolic pathways." Mol Gen Genet 193(3);437-44. PMID: 6423933

Mercenier80: Mercenier A, Simon JP, Haas D, Stalon V (1980). "Catabolism of L-arginine by Pseudomonas aeruginosa." J Gen Microbiol 116(2);381-9. PMID: 6768836

Nakada01: Nakada Y, Jiang Y, Nishijyo T, Itoh Y, Lu CD (2001). "Molecular characterization and regulation of the aguBA operon, responsible for agmatine utilization in Pseudomonas aeruginosa PAO1." J Bacteriol 183(22);6517-24. PMID: 11673419

Nakada03: Nakada Y, Itoh Y (2003). "Identification of the putrescine biosynthetic genes in Pseudomonas aeruginosa and characterization of agmatine deiminase and N-carbamoylputrescine amidohydrolase of the arginine decarboxylase pathway." Microbiology 149(Pt 3);707-14. PMID: 12634339

Piotrowski03: Piotrowski M, Janowitz T, Kneifel H (2003). "Plant C-N hydrolases and the identification of a plant N-carbamoylputrescine amidohydrolase involved in polyamine biosynthesis." J Biol Chem 278(3);1708-12. PMID: 12435743

Smith64: Smith, T. A., Garraway, J. L. (1964). "N-carbamylputrescine - an intermediate in the formation of putrescine by barley." Pytochemistry 3:23-26.

Stalon82: Stalon V, Simon JP, Mercenier A (1982). "Enzymes of arginine utilization and their formation in Aeromonas formicans NCIB 9232." Arch Microbiol 133(4);295-9. PMID: 6303241

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

Bell90: Bell E, Malmberg RL (1990). "Analysis of a cDNA encoding arginine decarboxylase from oat reveals similarity to the Escherichia coli arginine decarboxylase and evidence of protein processing." Mol Gen Genet 224(3);431-6. PMID: 2266946

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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Forouhar10: Forouhar F, Lew S, Seetharaman J, Xiao R, Acton TB, Montelione GT, Tong L (2010). "Structures of bacterial biosynthetic arginine decarboxylases." Acta Crystallogr Sect F Struct Biol Cryst Commun 66(Pt 12);1562-6. PMID: 21139196

Fukuda08: Fukuda W, Morimoto N, Imanaka T, Fujiwara S (2008). "Agmatine is essential for the cell growth of Thermococcus kodakaraensis." FEMS Microbiol Lett 287(1);113-20. PMID: 18702616

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

Hanfrey11: Hanfrey CC, Pearson BM, Hazeldine S, Lee J, Gaskin DJ, Woster PM, Phillips MA, Michael AJ (2011). "Alternative spermidine biosynthetic route is critical for growth of Campylobacter jejuni and is the dominant polyamine pathway in human gut microbiota." J Biol Chem 286(50);43301-12. PMID: 22025614

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

Janowitz03: Janowitz T, Kneifel H, Piotrowski M (2003). "Identification and characterization of plant agmatine iminohydrolase, the last missing link in polyamine biosynthesis of plants." FEBS Lett 544(1-3);258-61. PMID: 12782327

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Mo02: Mo H, Pua EC (2002). "Up-regulation of arginine decarboxylase gene expression and accumulation of polyamines in mustard (Brassica juncea)in response to stress." Physiol Plant 114(3);439-449. PMID: 12060267

Morris66: Morris DR, Pardee AB (1966). "Multiple pathways of putrescine biosynthesis in Escherichia coli." J Biol Chem 241(13);3129-35. PMID: 5330264

Morris83: Morris DR, Boeker EA (1983). "Biosynthetic and biodegradative ornithine and arginine decarboxylases from Escherichia coli." Methods Enzymol 1983;94;125-34. PMID: 6353148

PerezAmador95: Perez-Amador MA, Carbonell J, Granell A (1995). "Expression of arginine decarboxylase is induced during early fruit development and in young tissues of Pisum sativum (L.)." Plant Mol Biol 28(6);997-1009. PMID: 7548836

Rastogi93: Rastogi R, Dulson J, Rothstein SJ (1993). "Cloning of tomato (Lycopersicon esculentum Mill.) arginine decarboxylase gene and its expression during fruit ripening." Plant Physiol 103(3);829-34. PMID: 8022938

Sabo74a: Sabo DL, Fischer EH (1974). "Chemical properties of Escherichia coli lysine decarboxylase including a segment of its pyridoxal 5'-phosphate binding site." Biochemistry 13(4);670-6. PMID: 4204273

Sekowska98: Sekowska A, Bertin P, Danchin A (1998). "Characterization of polyamine synthesis pathway in Bacillus subtilis 168." Mol Microbiol 1998;29(3);851-8. PMID: 9723923

Song10: Song J, Zhou C, Liu R, Wu X, Wu D, Hu X, Ding Y (2010). "Expression and purification of recombinant arginine decarboxylase (speA) from Escherichia coli." Mol Biol Rep 37(4);1823-9. PMID: 19603287

Showing only 20 references. To show more, press the button "Show all references".


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, biocyc14.