MetaCyc Pathway: allantoin degradation to glyoxylate III
Inferred from experiment

Enzyme View:

Pathway diagram: allantoin degradation to glyoxylate III

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/AssimilationAmines and Polyamines DegradationAllantoin Degradation

Some taxa known to possess this pathway include : Bacillus fastidiosus, Escherichia coli K-12 substr. MG1655, Glycine max, Phaseolus vulgaris

Expected Taxonomic Range: Bacteria , Viridiplantae

General Background

Allantoin is a common product of purine degradation. Allantoin is rich in nitrogen, and many organisms are able to degrade and recycle it. Some bacteria, including Bacillus fastidiosus, Delftia acidovorans and Ralstonia eutropha JMP134, do so under aerobic conditions, while others such as Escherichia coli K-12, Streptococcus allantoicus and Providencia rettgeri do so only anaerobically.

Allantoin degradation is not limited to bacteria. Ureide-transporting plants convert fixed nitrogen in their roots to allantoin and allantoate, which are then transported to upper parts of the plant, where they are degraded to release the nitrogen. In addition, some fungi and animals also degrade allantoin.

The first step of the pathway, catalyzed by allantoinase, comprises the hydrolysis of the internal amide bond of (S)-(+)-allantoin, forming allantoate [Vogels76]. This enzyme turned out to be common to all organisms that can degrade allantoin, and is the first step in all allantoin degradation pathways.

Allantoate is converted to S-ureidoglycolate via one of two routes. In the first route the nitrogen is liberated in a single step in the form of urea ( EC, while in the other route it is liberated in the form of ammonia in two steps, via the intermediate a (-)-ureidoglycine (starting with EC

The next step in the pathway is the conversion of S-ureidoglycolate to glyoxylate. Similarly, this conversion can proceed with the liberation of either urea ( EC or ammonia ( EC

Several combinations of these routes have been documented. Some organisms possess pathways that produce solely urea (see allantoin degradation to glyoxylate I), some produce only ammonia (see allantoin degradation to glyoxylate II), and some produce both (see allantoin degradation to glyoxylate III). In addition, some anaerobic organisms can degrade allantoin to oxalurate instead of glyoxylate (see allantoin degradation IV (anaerobic)).

About This Pathway

In this hybrid pathway allantoate amidohydrolase monomer and ureidoglycine aminohydrolase catalyze the first two steps, producing S-ureidoglycolate and ammonia, while ureidoglycolate lyase gives rise to glyoxylate and urea. This pathway has been clearly documented in enterobacteria, including Escherichia coli K-12 [Cusa99, Serventi10], and some other bacteria, such as Bacillus fastidiosus [Xu95e]. There has been an ongoing debate regarding which pathway(s) operate in plants, but some research suggests that the hybrid pathway may exist in Glycine max and Phaseolus vulgaris [Todd04, Raso07].

Subpathways: allantoin degradation to ureidoglycolate II (ammonia producing)

Variants: allantoin degradation IV (anaerobic), allantoin degradation to glyoxylate I, allantoin degradation to glyoxylate II, allantoin degradation to ureidoglycolate I (urea producing), superpathway of allantoin degradation in plants, superpathway of allantoin degradation in yeast

Unification Links: EcoCyc:PWY-5705

Created 12-Nov-2007 by Caspi R, SRI International


Bongaerts76: Bongaerts GP, Vogels GD (1976). "Uric acid degradation by Bacillus fastidiosus strains." J Bacteriol 125(2);689-97. PMID: 1245468

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

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

Serventi10: Serventi F, Ramazzina I, Lamberto I, Puggioni V, Gatti R, Percudani R (2010). "Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria." ACS Chem Biol 5(2);203-14. PMID: 20038185

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

Vogels76: Vogels GD, Van der Drift C (1976). "Degradation of purines and pyrimidines by microorganisms." Bacteriol Rev 40(2);403-68. PMID: 786256

Xu95e: Xu Z, de Windt FE, van der Drift C (1995). "Purification and characterization of allantoate amidohydrolase from Bacillus fastidiosus." Arch Biochem Biophys 324(1);99-104. PMID: 7503567

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

Agarwal07: Agarwal R, Burley SK, Swaminathan S (2007). "Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics." J Mol Biol 368(2);450-63. PMID: 17362992

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

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

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

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

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."

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

Kim00b: 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

Kim09a: 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."

Mulrooney03: Mulrooney SB, Hausinger RP (2003). "Metal ion dependence of recombinant Escherichia coli allantoinase." J Bacteriol 185(1);126-34. PMID: 12486048

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

Percudani13: Percudani R, Carnevali D, Puggioni V (2013). "Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa." Database (Oxford) 2013;bat071. PMID: 24107613

Puggioni14: Puggioni V, Dondi A, Folli C, Shin I, Rhee S, Percudani R (2014). "Gene context analysis reveals functional divergence between hypothetically equivalent enzymes of the purine-ureide pathway." Biochemistry 53(4);735-45. PMID: 24417435

Rintoul02: Rintoul MR, Cusa E, Baldoma L, Badia J, Reitzer L, Aguilar J (2002). "Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS." J Mol Biol 324(4);599-610. PMID: 12460564

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

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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