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discounted EARLY registration ends Dec 31, 2014
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discounted EARLY registration ends Dec 31, 2014
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MetaCyc Chimeric Pathway: superpathway of allantoin degradation in plants

Enzyme View:

Note: a dashed line (without arrowheads) between two compound names is meant to imply that the two names are just different instantiations of the same compound -- i.e. one may be a specific name and the other a general name, or they may both represent the same compound in different stages of a polymerization-type pathway. 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.

Synonyms: ureide degradation

Superclasses: Degradation/Utilization/Assimilation Amines and Polyamines Degradation Allantoin Degradation
Superpathways

Some taxa known to possess parts of the pathway include ? : Arabidopsis thaliana col , Chlamydomonas reinhardtii Inferred from experiment [Pineda94], Cicer arietinum , Glycine max , Phaseolus vulgaris , Robinia pseudoacacia

Expected Taxonomic Range: Viridiplantae

Note: This is a chimeric pathway, comprising reactions from multiple organisms, and typically will not occur in its entirety in a single organism. The taxa listed here are likely to catalyze only subsets of the reactions depicted in this pathway.

Summary:
General Background

The ureides allantoin and allantoate are the major nitrogenous compounds synthesized in root nodules of ureide exporting legumes, such as soybean, during nitrogen fixation. Synthesized ureides are transported from root nodules via the xylem to shoots, where they are rapidly degraded. The products of ureide catabolism are re-assimilated and utilized in nitrogen metabolism.

Early reports about allantoin degradation in Glycine max found that different cultivars were utilizing different routes [Winkler85, Shelp85, Winkler87, Winkler88, Vadez00]. However, a later study concluded that the previous investigations may have been misled by side effects of the enzyme inhibitor used, and that both cultivars were utilizing the same degradation pathway. In both cases the route from allantoate to S-ureidoglycolate involved the production of ammonia, while urea was produced later in the pathway, by ureidoglycolate urea-lyase (EC 4.3.2.3) [Todd04]. The later activity was also described in Cicer arietinum (chickpea), an amide transporter [Munoz01]. These conclusions were supported by the isolation of allantoate amidohydrolase and ureidoglycolate amidohydrolase from Phaseolus vulgaris [Raso07, Munoz06].

On the other hand, a conflicting report of ammonia-producing conversion of S-ureidoglycolate to glyoxylate by ureidoglycolate amidohydrolase (EC 3.5.3.19) in Phaseolus vulgaris has been reported [Wells91].

Complicating things further, an allantoicase (EC 3.5.3.4) has been purified from the green alga Chlamydomonas reinhardtii, suggesting the existence of additional allantoin degradation routes in green algae [Piedras00].

Summary

There is some uncertainty about the ureide degradation pathway in nitrogen fixing plants, since several routes are possible. The general scheme of the pathway is the degradation of (S)-(+)-allantoin via allantoate to S-ureidoglycolate, which is degraded futher into glyoxylate.

However, there are two possible routes leading from allantoate to S-ureidoglycolate, and there are two possible routes from S-ureidoglycolate to glyoxylate: each of these two steps can be performed by enzyme(s) that liberate the nitrogen as either ammonia or urea.

The ammonia-producing enzymes are allantoate amidohydrolase (EC 3.5.3.9), which converts allantoate to S-ureidoglycolate via a (-)-ureidoglycine, and ureidoglycolate amidohydrolase (EC 3.5.3.19), which converts S-ureidoglycolate to glyoxylate.

The urea-producing enzymes are allantoicase (EC 3.5.3.4), which converts allantoate directly to S-ureidoglycolate, and ureidoglycolate urea-lyase (EC 4.3.2.3), which converts S-ureidoglycolate to glyoxylate.

Citations: [Piedras95]

Subpathways: allantoin degradation to ureidoglycolate II (ammonia producing) , allantoin degradation to glyoxylate I , allantoin degradation to glyoxylate II , urea degradation II , allantoin degradation to ureidoglycolate I (urea producing)

Variants: allantoin degradation IV (anaerobic) , allantoin degradation to glyoxylate III , superpathway of allantoin degradation in yeast

Unification Links: AraCyc:URDEGR-PWY

Credits:
Created 13-Aug-1999 by Iourovitski I , SRI International
Revised 07-Sep-2006 by Caspi R , SRI International
Revised 09-Nov-2007 by Caspi R , SRI International


References

Munoz01: Munoz A, Piedras P, Aguilar M, Pineda M (2001). "Urea Is a Product of Ureidoglycolate Degradation in Chickpea. Purification and Characterization of the Ureidoglycolate Urea-Lyase." Plant Physiol 2001;125(2);828-834. PMID: 11161040

Munoz06: Munoz A, Raso MJ, Pineda M, Piedras P (2006). "Degradation of ureidoglycolate in French bean (Phaseolus vulgaris) is catalysed by a ubiquitous ureidoglycolate urea-lyase." Planta 224(1);175-84. PMID: 16333637

Piedras00: Piedras P, Munoz A, Aguilar M, Pineda M (2000). "Allantoate amidinohydrolase (Allantoicase) from Chlamydomonas reinhardtii: its purification and catalytic and molecular characterization." Arch Biochem Biophys 378(2);340-8. PMID: 10860551

Piedras95: Piedras, P, Cardenas, J, Pineda, M (1995). "Solubilization and extraction of allantoinase and allantoicase from the green alga Chlamydomonas reinhardtii." Phytochemical Analysis.6(5):239-243.

Pineda94: Pineda M, Piedras P, Cardenas J (1994). "A continuous spectrophotometric assay for ureidoglycolase activity with lactate dehydrogenase or glyoxylate reductase as coupling enzyme." Anal Biochem 222(2);450-5. PMID: 7864371

Raso07: Raso MJ, Munoz A, Pineda M, Piedras P (2007). "Biochemical characterisation of an allantoate-degrading enzyme from French bean (Phaseolus vulgaris): the requirement of phenylhydrazine." Planta 226(5);1333-42. PMID: 17594111

Shelp85: Shelp BJ, Ireland RJ (1985). "Ureide Metabolism in Leaves of Nitrogen-Fixing Soybean Plants." Plant Physiol 77(3);779-783. PMID: 16664133

Todd04: Todd CD, Polacco JC (2004). "Soybean cultivars 'Williams 82' and 'Maple Arrow' produce both urea and ammonia during ureide degradation." J Exp Bot 55(398);867-77. PMID: 15020640

Todd06: Todd CD, Tipton PA, Blevins DG, Piedras P, Pineda M, Polacco JC (2006). "Update on ureide degradation in legumes." J Exp Bot 57(1);5-12. PMID: 16317038

Vadez00: Vadez V, Sinclair TR (2000). "Ureide degradation pathways in intact soybean leaves." J Exp Bot 2000;51(349);1459-65. PMID: 10944160

Wells91: Wells XE, Lees EM (1991). "Ureidoglycolate amidohydrolase from developing French bean fruits (Phaseolus vulgaris [L.].)." Arch Biochem Biophys 1991;287(1);151-9. PMID: 1910298

Winkler85: Winkler RG, Polacco JC, Blevins DG, Randall DD (1985). "Enzymic Degradation of Allantoate in Developing Soybeans." Plant Physiol 79(3);787-793. PMID: 16664492

Winkler87: Winkler RG, Blevins DG, Polacco JC, Randall DD (1987). "Ureide Catabolism of Soybeans : II. Pathway of Catabolism in Intact Leaf Tissue." Plant Physiol 83(3);585-591. PMID: 16665292

Winkler88: Winkler RG, Blevins DG, Randall DD (1988). "Ureide Catabolism in Soybeans : III. Ureidoglycolate Amidohydrolase and Allantoate Amidohydrolase Are Activities of an Allantoate Degrading Enzyme Complex." Plant Physiol 86(4);1084-1088. PMID: 16666035

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

Bauerfeind97: Bauerfeind P, Garner R, Dunn BE, Mobley HL (1997). "Synthesis and activity of Helicobacter pylori urease and catalase at low pH." Gut 40(1);25-30. PMID: 9155571

Benoit03: Benoit S, Maier RJ (2003). "Dependence of Helicobacter pylori urease activity on the nickel-sequestering ability of the UreE accessory protein." J Bacteriol 185(16);4787-95. PMID: 12896998

Benoit07: Benoit SL, Mehta N, Weinberg MV, Maier C, Maier RJ (2007). "Interaction between the Helicobacter pylori accessory proteins HypA and UreE is needed for urease maturation." Microbiology 153(Pt 5);1474-82. PMID: 17464061

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

Buckholz91: Buckholz RG, Cooper TG (1991). "The allantoinase (DAL1) gene of Saccharomyces cerevisiae." Yeast 7(9);913-23. PMID: 1803816

Burne00: Burne RA, Chen YY (2000). "Bacterial ureases in infectious diseases." Microbes Infect 2(5);533-42. PMID: 10865198

Campbell54: Campbell, L.L. (1954). "The mechanism of allantoin degradation by a Pseudomonas." J Bacteriol 68(5);598-603. PMID: 13211565

Campbell55: Campbell, L.L. (1955). "Oxidative degradation of uric acid by cell extracts of a Pseudomonas." Biochim Biophys Acta 18(1);160-1. PMID: 13260270

Chen00b: Chen YY, Weaver CA, Burne RA (2000). "Dual functions of Streptococcus salivarius urease." J Bacteriol 2000;182(16);4667-9. PMID: 10913107

Chen96a: Chen YY, Clancy KA, Burne RA (1996). "Streptococcus salivarius urease: genetic and biochemical characterization and expression in a dental plaque streptococcus." Infect Immun 1996;64(2);585-92. PMID: 8550211

Choi66: Choi KS, Lee KW, Roush AH (1966). "The assay of yeast ureidoglycolatase." Anal Biochem 17(3);413-22. PMID: 5965980

Cooper79: Cooper TG, Gorski M, Turoscy V (1979). "A cluster of three genes responsible for allantoin degradation in Saccharomyces cerevisiae." Genetics 92(2);383-96. PMID: 385448

Cusa99: Cusa E, Obradors N, Baldoma L, Badia J, Aguilar J (1999). "Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli." J Bacteriol 1999;181(24);7479-84. PMID: 10601204

Freyermuth00: Freyermuth SK, Bacanamwo M, Polacco JC (2000). "The soybean Eu3 gene encodes an Ni-binding protein necessary for urease activity." Plant J 2000;21(1);53-60. PMID: 10652150

Hanks81: Hanks JF, Tolbert NE, Schubert KR (1981). "Localization of Enzymes of Ureide Biosynthesis in Peroxisomes and Microsomes of Nodules." Plant Physiol 68(1);65-69. PMID: 16661891

Ho11: Ho YY, Hsieh HC, Huang CY (2011). "Biochemical characterization of allantoinase from Escherichia coli BL21." Protein J 30(6);384-94. PMID: 21739308

Kanamori04: Kanamori T, Kanou N, Atomi H, Imanaka T (2004). "Enzymatic characterization of a prokaryotic urea carboxylase." J Bacteriol 186(9);2532-9. PMID: 15090492

Kim00c: Kim GJ, Lee DE, Kim HS (2000). "Functional expression and characterization of the two cyclic amidohydrolase enzymes, allantoinase and a novel phenylhydantoinase, from Escherichia coli." J Bacteriol 2000;182(24);7021-8. PMID: 11092864

Kim09c: Kim K, Kim MI, Chung J, Ahn JH, Rhee S (2009). "Crystal structure of metal-dependent allantoinase from Escherichia coli." J Mol Biol 387(5);1067-74. PMID: 19248789

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

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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 Dec 22, 2014, biocyc13.