MetaCyc Pathway: superpathway of allantoin degradation in yeast
Inferred from experimentTraceable author statement to experimental support

Pathway diagram: superpathway of allantoin degradation in yeast

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/AssimilationAmines and Polyamines DegradationAllantoin Degradation

Some taxa known to possess this pathway include : Saccharomyces cerevisiae

Expected Taxonomic Range: Fungi

This allantoin degradation pathway, which converts (S)-(+)-allantoin to ammonia and CO2, allows Saccharomyces cerevisiae to use allantoin as a sole nitrogen source. (S)-(+)-allantoin is converted to glyoxylate by the DAL1, DAL2, and DAL3 gene products, which work sequentially to liberate the nitrogen from (S)-(+)-allantoin is the form of two urea molecules [Yoo85]. Urea is then degraded to ammonia in a two-step process by urea amidolyase, a multifunctional single enzyme encoded by the DUR1,2 gene. This enzyme was originally thought to be encoded by two tightly-linked genes (hence the name DUR1,2) [Cooper80].

The allantoin catabolic pathway genes are regulated by a general signal that responds to the availability of readily utilizable nitrogen sources, and also by pathway-specific induction by (S)-(+)-allantoin or by the intermediate urea-1-carboxylate. These regulatory effects are mediated by cis-acting DNA elements and the trans-acting factors Gln3p, Gat1p, Dal80p, Dal81p, and Dal82p [Rai99, Magasanik02, Scott00, Talibi95].

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

Variants: allantoin degradation IV (anaerobic), allantoin degradation to glyoxylate II, allantoin degradation to glyoxylate III, allantoin degradation to ureidoglycolate II (ammonia producing), superpathway of allantoin degradation in plants

Created 27-Apr-2005 by Hong E, Balakrishnan R, Saccharomyces Genome Database
Reviewed 03-Apr-2006 by Caspi R, SRI International
Revised 09-Nov-2007 by Caspi R, SRI International


Cooper80: Cooper TG, Lam C, Turoscy V (1980). "Structural analysis of the dur loci in S. cerevisiae: two domains of a single multifunctional gene." Genetics 94(3);555-80. PMID: 6105114

Magasanik02: Magasanik B, Kaiser CA (2002). "Nitrogen regulation in Saccharomyces cerevisiae." Gene 290(1-2);1-18. PMID: 12062797

Rai99: Rai R, Daugherty JR, Cunningham TS, Cooper TG (1999). "Overlapping positive and negative GATA factor binding sites mediate inducible DAL7 gene expression in Saccharomyces cerevisiae." J Biol Chem 274(39);28026-34. PMID: 10488154

Scott00: Scott S, Dorrington R, Svetlov V, Beeser AE, Distler M, Cooper TG (2000). "Functional domain mapping and subcellular distribution of Dal82p in Saccharomyces cerevisiae." J Biol Chem 275(10);7198-204. PMID: 10702289

Talibi95: Talibi D, Grenson M, Andre B (1995). "Cis- and trans-acting elements determining induction of the genes of the gamma-aminobutyrate (GABA) utilization pathway in Saccharomyces cerevisiae." Nucleic Acids Res 23(4);550-7. PMID: 7899074

Yoo85: Yoo HS, Genbauffe FS, Cooper TG (1985). "Identification of the ureidoglycolate hydrolase gene in the DAL gene cluster of Saccharomyces cerevisiae." Mol Cell Biol 5(9);2279-88. PMID: 3915539

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

Bossinger74: Bossinger J, Lawther RP, Cooper TG (1974). "Nitrogen repression of the allantoin degradative enzymes in Saccharomyces cerevisiae." J Bacteriol 118(3);821-9. PMID: 4598006

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

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

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

Genbauffe91: Genbauffe FS, Cooper TG (1991). "The urea amidolyase (DUR1,2) gene of Saccharomyces cerevisiae." DNA Seq 2(1);19-32. PMID: 1802034

Hayashi00: Hayashi S, Fujiwara S, Noguchi T (2000). "Evolution of urate-degrading enzymes in animal peroxisomes." Cell Biochem Biophys 32 Spring;123-9. PMID: 11330038

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

Kim00a: 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

Kim09: 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."

Leulliot04: Leulliot N, Quevillon-Cheruel S, Sorel I, Graille M, Meyer P, Liger D, Blondeau K, Janin J, van Tilbeurgh H (2004). "Crystal structure of yeast allantoicase reveals a repeated jelly roll motif." J Biol Chem 279(22);23447-52. PMID: 15020593

Mackay82: Mackay EM, Pateman JA (1982). "The regulation of urease activity in Aspergillus nidulans." Biochem Genet 20(7-8);763-76. PMID: 6753831

Matsumoto78: Matsumoto H, Ohta S, Kobayashi R, Terawaki Y (1978). "Chromosomal location of genes participating in the degradation of purines in Pseudomonas aeruginosa." Mol Gen Genet 167(2);165-76. PMID: 104142

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

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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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