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Escherichia coli K-12 substr. MG1655 Pathway: allantoin degradation IV (anaerobic)
Inferred from experiment

Pathway diagram: allantoin degradation IV (anaerobic)

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Schematic showing all replicons, marked with selected genes

Genetic Regulation Schematic

Genetic regulation schematic for allantoin degradation IV (anaerobic)

Superclasses: Degradation/Utilization/AssimilationAmines and Polyamines DegradationAllantoin Degradation

(S)-(+)-allantoin is a common product of purine degradation. Escherichia coli K-12 substr. MG1655 is able to utilize (S)-(+)-allantoin as a sole source of nitrogen under anaerobic conditions, but can not utilize it as a sole source of carbon [Cusa99].

The first step in allantoin degradation is the opening of the aromatic ring, yielding allantoate, performed by allantoinase. In the next step allantoate is hydrolyzed to S-ureidoglycine by allantoate amidohydrolase. While the second hydrolysis step (from S-ureidoglycine to S-ureidoglycolate) can happen spontaneously in a non-stereospecific manner, it is stereospecifically catalyzed by S-ureidoglycine aminohydrolase.

ureidoglycolate dehydrogenase then oxidizes ureidoglycolate to oxalurate. While not proven unequivocally in E. coli, it is believed oxalurate is converted into oxamate and carbamoyl phosphate, which can be further metabolized to CO2, ammonia and ATP [Cusa99].

The variant pathway allantoin degradation to glyoxylate III shows a possible alternative route of allantoin degradation, where the ureidoglycolate intermediate is processed differently. The enzyme ureidoglycolate lyase can convert ureidoglycolate to glyoxylate and urea; glyoxylate could then enter general metabolism, where it would be converted by the successive action of three enzymes to 3-phosphoglycerate, feeding into glycolysis I (from glucose 6-phosphate) (see glycolate and glyoxylate degradation I). However, this route would imply that allantoin can serve as a sole source of carbon in E. coli, which it can not. Additionally, ureidoglycolate lyase is poorly characterized.

Subpathways: allantoin degradation to ureidoglycolate II (ammonia producing)

Variants: allantoin degradation to glyoxylate III

Created 28-Feb-2000 by Pellegrini-Toole A, Marine Biological Laboratory
Revised 22-Aug-2007 by Keseler I, SRI International
Revised 06-Nov-2007 by Caspi R, SRI International
Revised 21-Mar-2008 by Keseler I, SRI International
Revised 04-Jan-2010 by Keseler I, SRI International
Last-Curated 21-Mar-2008 by Keseler I, SRI International


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

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.

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

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

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

Kim12: Kim MI, Shin I, Cho S, Lee J, Rhee S (2012). "Structural and functional insights into (s)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization." PLoS One 7(12);e52066. PMID: 23284870

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

ParadisBleau14: Paradis-Bleau C, Kritikos G, Orlova K, Typas A, Bernhardt TG (2014). "A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism." PLoS Genet 10(1);e1004056. PMID: 24391520

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

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

Shin14: Shin I, Han K, Rhee S (2014). "Structural Insights into the Substrate Specificity of (S)-Ureidoglycolate Amidohydrolase and Its Comparison with Allantoate Amidohydrolase." J Mol Biol. PMID: 25020232

Smith12: Smith AA, Belda E, Viari A, Medigue C, Vallenet D (2012). "The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes." PLoS Comput Biol 8(5);e1002540. PMID: 22693442

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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