Escherichia coli K-12 substr. MG1655 Enzyme: ureidoglycolate dehydrogenase

Gene: allD Accession Numbers: G6286 (EcoCyc), b0517, ECK0510

Synonyms: glxB8, ylbC

Regulation Summary Diagram: ?

Regulation summary diagram for allD

Subunit composition of ureidoglycolate dehydrogenase = [AllD]2
         ureidoglycolate dehydrogenase = AllD

Ureidoglycolate dehydrogenase (AllD) catalyzes the oxidation of ureidoglycolate to oxalurate, a final step in the assimilation of allantoin. 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].

Crystal structures of apo-AllD as well as binary and ternary complexes have been solved. Kinetic analysis of the wild-type and various mutant enzymes indicate that His116 acts as a general catalytic base; a reaction mechanism was proposed [Kim12d].

Ureidoglycolate dehydrogenase activity and allD transcription is induced by growth on allantoin as the sole source of nitrogen [Cusa99].

Locations: cytosol

Map Position: [544,538 <- 545,587] (11.74 centisomes, 42°)
Length: 1050 bp / 349 aa

Molecular Weight of Polypeptide: 37.967 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001780 , EchoBASE:EB3389 , EcoGene:EG13624 , EcoliWiki:b0517 , ModBase:P77555 , OU-Microarray:b0517 , PortEco:allD , PR:PRO_000022082 , Protein Model Portal:P77555 , RefSeq:NP_415050 , RegulonDB:G6286 , SMR:P77555 , String:511145.b0517 , UniProt:P77555

Relationship Links: InterPro:IN-FAMILY:IPR003767 , InterPro:IN-FAMILY:IPR017590 , Panther:IN-FAMILY:PTHR11091 , PDB:Structure:1XRH , PDB:Structure:4H8A , Pfam:IN-FAMILY:PF02615

In Paralogous Gene Group: 147 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for allD

GO Terms:

Biological Process: GO:0009442 - allantoin assimilation pathway Inferred from experiment [Cusa99]
GO:0000256 - allantoin catabolic process Inferred by computational analysis [UniProtGOA12]
GO:0006144 - purine nucleobase metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01a]
Molecular Function: GO:0009040 - ureidoglycolate dehydrogenase activity Inferred from experiment [Kim12d, Cusa99]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
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 allD 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]

Created 09-Jan-2013 by Keseler I , SRI International
Last-Curated ? 09-Jan-2013 by Keseler I , SRI International

Enzymatic reaction of: ureidoglycolate dehydrogenase

EC Number:

S-ureidoglycolate + NAD+ <=> oxalurate + NADH + 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 IV (anaerobic)

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Kim12d, BRENDA14]

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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


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."

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

GOA01a: 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

Kim12d: 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

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

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

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

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

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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 19.0 on Tue Oct 13, 2015, BIOCYC14A.