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Escherichia coli K-12 substr. MG1655 Enzyme: allantoate amidohydrolase



Gene: allC Accession Numbers: G6285 (EcoCyc), b0516, ECK0509

Synonyms: glxB7, ylbB

Regulation Summary Diagram: ?

Subunit composition of allantoate amidohydrolase = [AllC]2
         allantoate amidohydrolase monomer = AllC

Summary:
E. coli is able to utilize allantoin as a sole nitrogen source under anaerobic conditions [Cusa99]. Following (S)-(+)-allantoin ring opening, allantoate amidohydrolase converts allantoate to S-ureidoglycine, liberating one molecule each of ammonia and CO2 [Werner10, Serventi10]. Before the identification of S-ureidoglycine aminohydrolase, allantoate amidohydrolase was thought to catalyze both hydrolysis reactions of the allantoin degradation pathway, generating S-ureidoglycolate directly [Cusa99, Agarwal07].

The crystal structure of allantoate amidohydrolase has been solved at 2.25 Å resolution. It exists as a homodimer in solution and the crystal, with each polypeptide chain folded into two domains - a large catalytic domain containing two metal ions, sulfate, and substrate binding sites, and a smaller dimerization domain. Due to the overall similarity of the protein to the di-zinc-dependent metallopeptidases, the metal ions were thought to be zinc. The sulfate ion may be an allosteric effector. A reaction mechanism was proposed [Agarwal07]. A crystal structure of the catalytically inactive E126A mutant in complex with allantoate shows a large movement of the catalytic domain into a closed conformation [Shin14].

Allantoate amidohydrolase activity is induced by growth on allantoin as the sole source of nitrogen [Cusa99].

Locations: cytosol

Map Position: [543,281 <- 544,516] (11.71 centisomes)
Length: 1236 bp / 411 aa

Molecular Weight of Polypeptide: 45.694 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001777 , DIP:DIP-9088N , EchoBASE:EB3388 , EcoGene:EG13623 , EcoliWiki:b0516 , ModBase:P77425 , OU-Microarray:b0516 , PortEco:allC , PR:PRO_000022081 , Pride:P77425 , Protein Model Portal:P77425 , RefSeq:NP_415049 , RegulonDB:G6285 , SMR:P77425 , String:511145.b0516 , Swiss-Model:P77425 , UniProt:P77425

Relationship Links: InterPro:IN-FAMILY:IPR002933 , InterPro:IN-FAMILY:IPR010158 , InterPro:IN-FAMILY:IPR011650 , InterPro:IN-FAMILY:IPR017591 , PDB:Structure:1Z2L , PDB:Structure:2IMO , PDB:Structure:4PXD , Pfam:IN-FAMILY:PF01546

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009442 - allantoin assimilation pathway Inferred from experiment Inferred by computational analysis [GOA01, Werner10, Cusa99]
GO:0000256 - allantoin catabolic process Inferred by computational analysis [UniProtGOA12]
GO:0006144 - purine nucleobase metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0030145 - manganese ion binding Inferred from experiment Inferred by computational analysis [GOA01, Serventi10]
GO:0042803 - protein homodimerization activity Inferred from experiment Inferred by computational analysis [GOA01, Agarwal07]
GO:0047652 - allantoate deiminase activity Inferred from experiment Inferred by computational analysis [GOA01, Serventi10, Cusa99]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016813 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism allantoin assimilation
metabolism metabolism of other compounds nitrogen metabolism

Essentiality data for allC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Created 13-Nov-2007 by Caspi R , SRI International
Last-Curated ? 22-Jul-2014 by Keseler I , SRI International


Enzymatic reaction of: allantoate amidohydrolase

Synonyms: allantoate amidinohydrolase

EC Number: 3.5.3.9

allantoate + 2 H+ + H2O <=> S-ureidoglycine + ammonium + CO2

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: allantoin degradation to glyoxylate III , allantoin degradation IV (anaerobic) , allantoin degradation to ureidoglycolate II (ammonia producing)

Cofactors or Prosthetic Groups: Mn2+ [Werner10, Serventi10]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 83
[UniProt10]
UniProt: Zinc 1;
Metal-Binding-Site 92
[UniProt10]
UniProt: Zinc 1;
Metal-Binding-Site 127
[UniProt10]
UniProt: Zinc 2;
Metal-Binding-Site 190
[UniProt10]
UniProt: Zinc 1;
Metal-Binding-Site 382
[UniProt10]
UniProt: Zinc 2;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: 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."

Werner10: Werner AK, Romeis T, Witte CP (2010). "Ureide catabolism in Arabidopsis thaliana and Escherichia coli." Nat Chem Biol 6(1);19-21. PMID: 19935661

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 27, 2014, biocyc11.