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MetaCyc Pathway: putrescine biosynthesis II

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: Biosynthesis Amines and Polyamines Biosynthesis Putrescine Biosynthesis

Some taxa known to possess this pathway include ? : Aeromonas caviae , Arabidopsis thaliana col , Campylobacter jejuni jejuni 81116 , Pseudomonas aeruginosa

Expected Taxonomic Range: Firmicutes , Proteobacteria , Viridiplantae

Summary:
General Backround

The polyamines (the most common of which are putrescine, spermidine, and spermine) are a group of positively charged organic polycations that are involved in many biological processes, including binding to nucleic acids, stabilizing membranes, and stimulating several enzymes [Tabor85, Abraham68, Frydman92, Huang90b]. While it is clear that polyamines are essential for normal cell growth, we still do not fully understand their specific molecular functions in vivo [Tabor85]. putrescine and spermidine are found in all life forms, and spermine is found mostly in eukaryotes.

putrescine can be formed either directly from L-ornithine by ornithine decarboxylase (ODC) (see putrescine biosynthesis III) or indirectly from L-arginine by arginine decarboxylase (ADC) (see putrescine biosynthesis I and putrescine biosynthesis II). While the ODC pathway was considered the only mammalian pathway for polyamine biosynthesis, recently the presence of the ADC pathway in mammals has been demonstrated [Mistry02, Zhu04]. In higher plants the presence of both pathways has been known for some time [Galston90]. In bacteria, both pathways are common, and are often found side by side in the same organism [Tabor85].

About This Pathway

There are two flavors of the ADC pathway. In both cases L-arginine is first converted to agmatine by a biosynthetic arginine decarboxylase. However, in enterobacteria and mycobacteria agmatine is converted directly to putrescine by the enzyme agmatinase (see putrescine biosynthesis I), while in higher plants, Pseudomonas spp., Aeromonas spp., and lactic bacteria, agmatine is first hydrolyzed by agmatine deiminase into N-carbamoylputrescine and ammonia, and putrescine is formed by removal of the ureido group from N-carbamoylputrescine by the enzyme N-carbamoylputrescine amidohydrolase.

It should be mentioned that it has been suggested that in Pseudomonas aeruginosa this pathway can operate in a catabolic manner [Mercenier80, Cunin86, Nakada01], catalyzing the degradation of L-arginine through putrescine into succinate, supplying the bacteria with carbon and nitrogen (see arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)). Since the main catabolic arginine pathway in these bacteria is the succinyltransferase pathway (see arginine degradation II (AST pathway)), there is still some debate whether this is a true arginine degradation pathway. However, it is agreed that the last two steps of the pathway are used for catabolic agmatine degradation [Nakada03].

Superpathways: superpathway of polyamine biosynthesis II

Variants: putrescine biosynthesis I , putrescine biosynthesis III , putrescine biosynthesis IV

Unification Links: AraCyc:PWY-43

Credits:
Created 10-Oct-2005 by Caspi R , SRI International


References

Abraham68: Abraham KA (1968). "Studies on DNA-dependent RNA polymerase from Escherichia coli. 1. The mechanism of polyamine induced stimulation of enzyme activity." Eur J Biochem 5(1);143-6. PMID: 4873311

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

Frydman92: Frydman L, Rossomando PC, Frydman V, Fernandez CO, Frydman B, Samejima K (1992). "Interactions between natural polyamines and tRNA: an 15N NMR analysis." Proc Natl Acad Sci U S A 89(19);9186-90. PMID: 1409623

Galston90: Galston AW, Sawhney RK (1990). "Polyamines in plant physiology." Plant Physiol 94(2);406-10. PMID: 11537482

Huang90b: Huang SC, Panagiotidis CA, Canellakis ES (1990). "Transcriptional effects of polyamines on ribosomal proteins and on polyamine-synthesizing enzymes in Escherichia coli." Proc Natl Acad Sci U S A 87(9);3464-8. PMID: 2185470

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

Mistry02: Mistry SK, Burwell TJ, Chambers RM, Rudolph-Owen L, Spaltmann F, Cook WJ, Morris SM (2002). "Cloning of human agmatinase. An alternate path for polyamine synthesis induced in liver by hepatitis B virus." Am J Physiol Gastrointest Liver Physiol 282(2);G375-81. PMID: 11804860

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

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

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

Zhu04: Zhu MY, Iyo A, Piletz JE, Regunathan S (2004). "Expression of human arginine decarboxylase, the biosynthetic enzyme for agmatine." Biochim Biophys Acta 1670(2);156-64. PMID: 14738999

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

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

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

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 Tue Nov 25, 2014, biocyc13.