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Escherichia coli K-12 substr. MG1655 Polypeptide: fused predicted xanthine/hypoxanthine oxidase: molybdopterin-binding subunit and Fe-S binding subunit

Gene: xdhD Accession Numbers: G7500 (EcoCyc), b2881, ECK2877

Synonyms: ygfN

Regulation Summary Diagram

Regulation summary diagram for xdhD

Component of: predicted xanthine dehydrogenase (summary available)

XdhD has similarity to molybdenum cofactor-containing xanthine oxidases, including Drosophila melanogaster xanthine dehydrogenase and Desulfovibrio gigas aldehyde oxidoreductase and is predicted to catalyze oxidation of xanthine (with electron transfer to O2, rather than dehydrogenase activity with electron transfer to NAD or NADP) [Xi00].

An xdhD mutant exhibits sensitivity to adenine, which is indicative of a defect in purine salvage, but it does not exhibit a defect in an indirect assay of xanthine dehydrogenase activity [Xi00, Neumann09]. Deletion of xdhD does not confer N-hydroxylaminopurine sensitivity [Kozmin07]. An xdhD null mutant is able to reduce selenate to elemental red selenium [Guymer09].

Locations: cytosol

Map Position: [3,019,338 -> 3,022,208] (65.08 centisomes, 234°)
Length: 2871 bp / 956 aa

Molecular Weight of Polypeptide: 103.52 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009459, DIP:DIP-28056N, EchoBASE:EB2876, EcoGene:EG13064, EcoliWiki:b2881, ModBase:Q46814, OU-Microarray:b2881, PortEco:xdhD, Pride:Q46814, Protein Model Portal:Q46814, RefSeq:NP_417357, RegulonDB:G7500, SMR:Q46814, String:511145.b2881, UniProt:Q46814

Relationship Links: InterPro:IN-FAMILY:IPR000674, InterPro:IN-FAMILY:IPR002888, InterPro:IN-FAMILY:IPR008274, InterPro:IN-FAMILY:IPR017699, Pfam:IN-FAMILY:PF01315, Pfam:IN-FAMILY:PF01799, Pfam:IN-FAMILY:PF02738, Smart:IN-FAMILY:SM01008

In Paralogous Gene Group: 86 (5 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

GO Terms:
Biological Process:
Inferred by computational analysisGO:0006144 - purine nucleobase metabolic process [UniProtGOA11a]
Inferred by computational analysisGO:0006166 - purine ribonucleoside salvage [UniProtGOA11a]
Inferred by computational analysisGO:0009115 - xanthine catabolic process [Gaudet10]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0005506 - iron ion binding [Sevcenco11]
Inferred by computational analysisGO:0004854 - xanthine dehydrogenase activity [Gaudet10]
Inferred by computational analysisGO:0004855 - xanthine oxidase activity [Gaudet10]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016903 - oxidoreductase activity, acting on the aldehyde or oxo group of donors [Gaudet10]
Inferred by computational analysisGO:0043546 - molybdopterin cofactor binding [Gaudet10]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0050660 - flavin adenine dinucleotide binding [Gaudet10]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a]
Inferred by computational analysisGO:0051537 - 2 iron, 2 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [Gaudet10]

MultiFun Terms: metabolismbiosynthesis of building blocksnucleotides

Essentiality data for xdhD knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated 02-Feb-2012 by Keseler I, SRI International

Subunit of: predicted xanthine dehydrogenase

Subunit composition of predicted xanthine dehydrogenase = [XdhD][YgfM]
         fused predicted xanthine/hypoxanthine oxidase: molybdopterin-binding subunit and Fe-S binding subunit = XdhD (summary available)
         predicted oxidoreductase = YgfM (summary available)

XdhD and YgfM are predicted to form a complex with xanthine dehydrogenase activity.

Sequence Features

Protein sequence of fused predicted xanthine/hypoxanthine oxidase: molybdopterin-binding subunit and Fe-S binding subunit with features indicated

Feature Class Location Citations Comment
Pfam PF01799 73 -> 145
Inferred by computational analysis[Finn14]
Fer2_2 : [2Fe-2S] binding domain
Pfam PF01315 187 -> 298
Inferred by computational analysis[Finn14]
Ald_Xan_dh_C : Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
Pfam PF02738 353 -> 893
Inferred by computational analysis[Finn14]
Ald_Xan_dh_C2 : Molybdopterin-binding domain of aldehyde dehydrogenase
Metal-Binding-Site 414
Inferred by computational analysis[UniProt15]
UniProt: Molybdenum.
Metal-Binding-Site 445
Inferred by computational analysis[UniProt15]
UniProt: Molybdenum; via carbonyl oxygen.
Metal-Binding-Site 727
Inferred by computational analysis[UniProt15]
UniProt: Molybdenum; via amide nitrogen.

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

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.
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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Guymer09: Guymer D, Maillard J, Sargent F (2009). "A genetic analysis of in vivo selenate reduction by Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12." Arch Microbiol 191(6);519-28. PMID: 19415239

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

Kozmin07: Kozmin SG, Schaaper RM (2007). "Molybdenum cofactor-dependent resistance to N-hydroxylated base analogs in Escherichia coli is independent of MobA function." Mutat Res 619(1-2);9-15. PMID: 17349664

Neumann09: 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

Sevcenco11: Sevcenco AM, Pinkse MW, Wolterbeek HT, Verhaert PD, Hagen WR, Hagedoorn PL (2011). "Exploring the microbial metalloproteome using MIRAGE." Metallomics 3(12);1324-30. PMID: 22094925

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

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

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

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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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