Escherichia coli K-12 substr. MG1655 Polypeptide: xanthine dehydrogenase subunit

Gene: xdhA Accession Numbers: G7485 (EcoCyc), b2866, ECK2862

Synonyms: ygeS

Regulation Summary Diagram: ?

Regulation summary diagram for xdhA

Component of: xanthine dehydrogenase (summary available)

XdhA has similarity to the molybdenum cofactor-containing domains of Drosophila melanogaster xanthine dehydrogenase and Desulfovibrio gigas aldehyde oxidoreductase [Xi00].

An xdhA mutant exhibits a defect in an indirect assay of xanthine dehydrogenase activity and exhibits sensitivity to adenine, which is indicative of a defect in purine salvage [Xi00]. The mutant exhibits more rapid growth than wild type utilizing aspartate as the source of nitrogen and growth under these conditions is stimulated by hypoxanthine [Xi00]. The mutant shows wild-type growth utilizing abundant ammonia as the nitrogen source [Xi00].

Citations: [Serres01]

Locations: cytosol

Map Position: [2,998,367 -> 3,000,625] (64.62 centisomes, 233°)
Length: 2259 bp / 752 aa

Molecular Weight of Polypeptide: 81.321 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009413 , EchoBASE:EB2861 , EcoGene:EG13049 , EcoliWiki:b2866 , ModBase:Q46799 , OU-Microarray:b2866 , PortEco:xdhA , PR:PRO_000024231 , Pride:Q46799 , Protein Model Portal:Q46799 , RefSeq:NP_417342 , RegulonDB:G7485 , SMR:Q46799 , String:511145.b2866 , UniProt:Q46799

Relationship Links: InterPro:IN-FAMILY:IPR000674 , InterPro:IN-FAMILY:IPR008274 , Pfam:IN-FAMILY:PF01315 , Pfam:IN-FAMILY:PF02738 , Smart:IN-FAMILY:SM01008

In Paralogous Gene Group: 86 (5 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for xdhA

GO Terms:

Biological Process: GO:0006144 - purine nucleobase metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006166 - purine ribonucleoside salvage Inferred by computational analysis [UniProtGOA11a]
GO:0009114 - hypoxanthine catabolic process Inferred by computational analysis [UniProtGOA12]
GO:0009115 - xanthine catabolic process Inferred by computational analysis [Gaudet10]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004854 - xanthine dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA01, Xi00]
GO:0016491 - oxidoreductase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Xi00]
GO:0004855 - xanthine oxidase activity Inferred by computational analysis [Gaudet10]
GO:0016903 - oxidoreductase activity, acting on the aldehyde or oxo group of donors Inferred by computational analysis [Gaudet10]
GO:0043546 - molybdopterin cofactor binding Inferred by computational analysis [Gaudet10]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0050660 - flavin adenine dinucleotide binding Inferred by computational analysis [Gaudet10]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [Gaudet10]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides

Essentiality data for xdhA 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]

Subunit of: xanthine dehydrogenase

Subunit composition of xanthine dehydrogenase = [XdhA][XdhB][XdhC]
         xanthine dehydrogenase subunit = XdhA (summary available)
         xanthine dehydrogenase subunit, FAD-binding domain = XdhB (summary available)
         xanthine dehydrogenase, Fe-S subunit = XdhC (summary available)

XdhA-XdhB-XdhC is a putative heterotrimeric xanthine dehydrogenase [Xi00].

Degradation of hypoxanthine, xanthosine, inosine, or allantoin does not provide adequate nitrogen to support cell growth under aerobic conditions, in contrast to degradation of adenine or adenosine, which does support cell growth [Xi00]. Hypoxanthine, guanosine, inosine, or xanthosine (but not allantoin) speeds the growth of cells utilizing aspartate as the nitrogen source [Xi00].

Xanthine degradation to allantoin has been observed [Xi00].

It is suggested that xanthine dehydrogenase plays a role in purine salvage, perhaps by favoring production of GMP rather than AMP [Xi00].

Last-Curated ? 12-Dec-2011 by Fulcher C , SRI International

Enzymatic reaction of: xanthine:NAD+ oxidoreductase (xanthine dehydrogenase)

EC Number:

xanthine + NAD+ + H2O <=> urate + 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: guanosine nucleotides degradation III , adenosine nucleotides degradation II

Cofactors or Prosthetic Groups: cytidylyl molybdenum cofactor [Neumann09a]

Enzymatic reaction of: hypoxanthine hydroxylase (xanthine dehydrogenase)

EC Number:

hypoxanthine + NAD+ + H2O <=> xanthine + 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: adenosine nucleotides degradation II

Sequence Features

Protein sequence of xanthine dehydrogenase subunit with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 206
UniProt: Molybdenum; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 237
UniProt: Molybdenum; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 350
UniProt: Molybdenum; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 516
UniProt: Molybdenum; via amide nitrogen; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
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

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

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

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, 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."

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

Neumann09a: Neumann M, Mittelstadt G, Seduk F, Iobbi-Nivol C, Leimkuhler S (2009). "MocA is a specific cytidylyl transferase involved in molybdopterin cytosine dinucleotide biosynthesis in Escherichia coli." J Biol Chem 284(33);21891-8. PMID: 19542235

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

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."

Xi00: Xi H, Schneider BL, Reitzer L (2000). "Purine catabolism in Escherichia coli and function of xanthine dehydrogenase in purine salvage." J Bacteriol 182(19);5332-41. PMID: 10986234

Other References Related to Gene Regulation

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

Zhao10: Zhao K, Liu M, Burgess RR (2010). "Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis." Nucleic Acids Res 38(4);1273-83. PMID: 19969540

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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, biocyc13.