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Escherichia coli K-12 substr. MG1655 Enzyme: allantoinase



Gene: allB Accession Numbers: G6281 (EcoCyc), b0512, ECK0505

Synonyms: glxB3, ybbX

Regulation Summary Diagram: ?

Subunit composition of allantoinase = [AllB]4
         allantoinase monomer = AllB

Summary:
Allantoinase catalyzes the hydrolytic ring cleavage of allantoin at the amide bond between N3 and C4, the first step in the assimilation of allantoin. The enzyme has a very narrow substrate specificity [Kim00d, Mulrooney03].

E. coli is able to utilize allantoin as a sole source of nitrogen under anaerobic conditions, but can not utilize it as a sole source of carbon [Cusa99].

A crystal structure of allantoinase has been solved at 2.1 Å resolution. The active site residues Asn94 and Ser317 are important for enzymatic activity [Kim09a].

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

Locations: cytosol

Map Position: [538,371 -> 539,732] (11.6 centisomes)
Length: 1362 bp / 453 aa

Molecular Weight of Polypeptide: 49.602 kD (from nucleotide sequence), 50.5 kD (experimental) [Kim00d ]

Molecular Weight of Multimer: 230.0 kD (experimental) [Kim00d]

Unification Links: ASAP:ABE-0001768 , EchoBASE:EB3384 , EcoGene:EG13619 , EcoliWiki:b0512 , ModBase:P77671 , OU-Microarray:b0512 , PortEco:allB , PR:PRO_000022080 , Protein Model Portal:P77671 , RefSeq:NP_415045 , RegulonDB:G6281 , SMR:P77671 , String:511145.b0512 , UniProt:P77671

Relationship Links: InterPro:IN-FAMILY:IPR011059 , InterPro:IN-FAMILY:IPR017593 , PDB:Structure:3E74 , Pfam:IN-FAMILY:PF01979

In Paralogous Gene Group: 465 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009442 - allantoin assimilation pathway Inferred from experiment [Mulrooney03]
GO:0000256 - allantoin catabolic process Inferred by computational analysis [UniProtGOA12, GOA06, GOA01]
GO:0006144 - purine nucleobase metabolic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004038 - allantoinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Kim00d, Mulrooney03]
GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA01, Mulrooney03]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0050897 - cobalt ion binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Kim09a]
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 allB 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:
Last-Curated ? 05-Jan-2010 by Keseler I , SRI International


Enzymatic reaction of: allantoinase

Synonyms: allantoin amidohydrolase

EC Number: 3.5.2.5

(S)-(+)-allantoin + H2O <=> allantoate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

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

Summary:
Either Zn2+ or Co2+ can fulfill the cofactor requirement of the enzyme. The Zn2+-supplemented enzyme is selective for the S isomer of allantoin [Mulrooney03, Kim09a], while the Co2+-supplemented enzyme can also hydrolyze the R isomer at a slower rate. The kinetic properties of the enzyme change significantly with the metal cofactor. Values for the Zn2+-supplemented enzyme are reported below, since it likely represents the in vivo form [Mulrooney03].

Cofactors or Prosthetic Groups: Zn2+ [Kim09a, Mulrooney03], Co2+ [Mulrooney03, Kim00d]

Alternative Cofactors for Co2+: Mn2+ [Comment 5 ] , Ni2+ [Comment 5 ]

Inhibitors (Competitive): dithiothreitol [Mulrooney03]

Inhibitors (Unknown Mechanism): Cu2+ [Kim00d]

Kinetic Parameters:

Substrate
Km (μM)
Citations
(S)-(+)-allantoin
28600.0, 37500.0
[Kim09a, BRENDA14]
(S)-(+)-allantoin
5500.0, 6200.0, 7300.0, 9600.0
[Ho11, BRENDA14]
(S)-(+)-allantoin
19500.0, 79900.0, 17000.0
[Mulrooney03, BRENDA14]

T(opt): 55 °C [BRENDA14, Ho11], 40-45 °C [Kim00d]

pH(opt): 7-8 [Mulrooney03]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 59
[UniProt10]
UniProt: Zinc 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 61
[UniProt10]
UniProt: Zinc 1; Non-Experimental Qualifier: by similarity;
N6-carboxylysine-Modification 146
[UniProt11]
UniProt: N6-carboxylysine; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 146
[UniProt10]
UniProt: Zinc 1; via carbamate group; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 186
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 242
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 315
[UniProt10]
UniProt: Zinc 1; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

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


References

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

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

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

Kim00d: 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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 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."

Other References Related to Gene Regulation

Hasegawa08: Hasegawa A, Ogasawara H, Kori A, Teramoto J, Ishihama A (2008). "The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines." Microbiology 154(Pt 11);3366-78. PMID: 18957590

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

Teramoto10: Teramoto J, Yamanishi Y, Magdy el-SH, Hasegawa A, Kori A, Nakajima M, Arai F, Fukuda T, Ishihama A (2010). "Single live-bacterial cell assay of promoter activity and regulation." Genes Cells 15(11);1111-22. PMID: 20964794


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 Mon Nov 24, 2014, BIOCYC13B.