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Q6AUV1

- XDH_ORYSJ

UniProt

Q6AUV1 - XDH_ORYSJ

Protein

Xanthine dehydrogenase

Gene

XDH

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 93 (01 Oct 2014)
      Sequence version 1 (13 Sep 2004)
      Previous versions | rss
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    Functioni

    Key enzyme involved in purine catabolism. Catalyzes the oxidation of hypoxanthine to xanthine and the oxidation of xanthine to urate By similarity.By similarity

    Catalytic activityi

    Xanthine + NAD+ + H2O = urate + NADH.
    Hypoxanthine + NAD+ + H2O = xanthine + NADH.

    Cofactori

    Binds 2 2Fe-2S clusters.By similarity
    FAD.By similarity
    Binds 1 molybdenum-molybdopterin (Mo-MPT) cofactor per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi58 – 581Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation
    Metal bindingi63 – 631Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation
    Metal bindingi66 – 661Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation
    Metal bindingi88 – 881Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation
    Metal bindingi128 – 1281Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation
    Metal bindingi131 – 1311Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation
    Metal bindingi164 – 1641Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation
    Metal bindingi166 – 1661Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation
    Binding sitei373 – 3731FADBy similarity
    Binding sitei396 – 3961FADBy similarity
    Binding sitei440 – 4401FAD; via amide nitrogen and carbonyl oxygenBy similarity
    Binding sitei458 – 4581FADBy similarity
    Metal bindingi804 – 8041MolybdenumBy similarity
    Metal bindingi835 – 8351Molybdenum; via carbonyl oxygenBy similarity
    Binding sitei839 – 8391SubstrateBy similarity
    Binding sitei917 – 9171SubstrateBy similarity
    Metal bindingi949 – 9491Molybdenum; via amide nitrogenBy similarity
    Binding sitei951 – 9511SubstrateBy similarity
    Binding sitei1047 – 10471SubstrateBy similarity
    Metal bindingi1116 – 11161Molybdenum; via amide nitrogenBy similarity
    Active sitei1305 – 13051Proton acceptorBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi293 – 3008FADBy similarity
    Nucleotide bindingi383 – 3875FADBy similarity

    GO - Molecular functioni

    1. 2 iron, 2 sulfur cluster binding Source: UniProtKB-KW
    2. electron carrier activity Source: InterPro
    3. flavin adenine dinucleotide binding Source: InterPro
    4. iron ion binding Source: InterPro
    5. UDP-N-acetylmuramate dehydrogenase activity Source: InterPro
    6. xanthine dehydrogenase activity Source: UniProtKB-EC

    GO - Biological processi

    1. response to reactive oxygen species Source: EnsemblPlants/Gramene
    2. response to water deprivation Source: EnsemblPlants/Gramene
    3. superoxide anion generation Source: EnsemblPlants/Gramene
    4. xanthine metabolic process Source: EnsemblPlants/Gramene

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    2Fe-2S, FAD, Flavoprotein, Iron, Iron-sulfur, Metal-binding, Molybdenum, NAD

    Enzyme and pathway databases

    ReactomeiREACT_223073. Vitamins B6 activation to pyridoxal phosphate.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Xanthine dehydrogenase (EC:1.17.1.4)
    Gene namesi
    Name:XDH
    Ordered Locus Names:Os03g0429800, LOC_Os03g31550
    ORF Names:OsJ_11360, OSJNBa0091B22.11
    OrganismiOryza sativa subsp. japonica (Rice)
    Taxonomic identifieri39947 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
    ProteomesiUP000000763: Chromosome 3

    Organism-specific databases

    GrameneiQ6AUV1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: EnsemblPlants/Gramene

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 13691369Xanthine dehydrogenasePRO_0000417459Add
    BLAST

    Proteomic databases

    PRIDEiQ6AUV1.

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ6AUV1.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini20 – 106872Fe-2S ferredoxin-typePROSITE-ProRule annotationAdd
    BLAST
    Domaini265 – 450186FAD-binding PCMH-typePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the xanthine dehydrogenase family.Curated
    Contains 1 2Fe-2S ferredoxin-type domain.PROSITE-ProRule annotation
    Contains 1 FAD-binding PCMH-type domain.PROSITE-ProRule annotation

    Phylogenomic databases

    HOGENOMiHOG000191197.
    KOiK00106.
    OMAiCDETFFA.

    Family and domain databases

    Gene3Di1.10.150.120. 1 hit.
    3.10.20.30. 1 hit.
    3.30.365.10. 6 hits.
    3.30.43.10. 1 hit.
    3.30.465.10. 1 hit.
    3.90.1170.50. 1 hit.
    InterProiIPR002888. 2Fe-2S-bd.
    IPR001041. 2Fe-2S_ferredoxin-type.
    IPR006058. 2Fe2S_fd_BS.
    IPR000674. Ald_Oxase/Xan_DH_a/b.
    IPR016208. Ald_Oxase/xanthine_DH.
    IPR008274. AldOxase/xan_DH_Mopterin-bd.
    IPR012675. Beta-grasp_dom.
    IPR005107. CO_DH_flav_C.
    IPR016169. CO_DH_flavot_FAD-bd_sub2.
    IPR016166. FAD-bd_2.
    IPR016167. FAD-bd_2_sub1.
    IPR002346. Mopterin_DH_FAD-bd.
    [Graphical view]
    PfamiPF01315. Ald_Xan_dh_C. 1 hit.
    PF02738. Ald_Xan_dh_C2. 1 hit.
    PF03450. CO_deh_flav_C. 1 hit.
    PF00941. FAD_binding_5. 1 hit.
    PF00111. Fer2. 1 hit.
    PF01799. Fer2_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000127. Xanthine_DH. 1 hit.
    SMARTiSM01008. Ald_Xan_dh_C. 1 hit.
    SM01092. CO_deh_flav_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF47741. SSF47741. 1 hit.
    SSF54292. SSF54292. 1 hit.
    SSF54665. SSF54665. 1 hit.
    SSF55447. SSF55447. 1 hit.
    SSF56003. SSF56003. 1 hit.
    SSF56176. SSF56176. 1 hit.
    PROSITEiPS00197. 2FE2S_FER_1. 1 hit.
    PS51085. 2FE2S_FER_2. 1 hit.
    PS51387. FAD_PCMH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q6AUV1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGSLTRAEEE ETAAAEEWSG EAVVYVNGVR RVLPDGLAHL TLLQYLRDIG     50
    LPGTKLGCGE GGCGACTVMV SCYDQTTKKT QHFAINACLA PLYSVEGMHI 100
    ITVEGIGNRQ RGLHPIQERL AMAHGSQCGF CTPGFVMSMY ALLRSSEQPP 150
    TEEQIEDSLA GNLCRCTGYR PIIDAFRVFS KRDDLLYNNS SLKNADGRPI 200
    CPSTGKPCSC GDQKDINGSE SSLLTPTKSY SPCSYNEIDG NAYSEKELIF 250
    PPELQLRKVT SLKLNGFNGI RWYRPLKLKQ VLHLKACYPN AKLIIGNSEV 300
    GVETKFKNAQ YKVLISVTHV PELHTLKVKE DGIHIGSSVR LAQLQNFLRK 350
    VILERDSHEI SSCEAILRQL KWFAGTQIRN VASVGGNICT ASPISDLNPL 400
    WMATGATFEI IDVNNNIRTI PAKDFFLGYR KVDLKPDEIL LSVILPWTRP 450
    FEFVKEFKQA HRREDDIALV NAGMRVYIRK VEGDWIISDV SIIYGGVAAV 500
    SHRASKTETF LTGKKWDYGL LDKTFDLLKE DVVLAENAPG GMVEFRSSLT 550
    LSFFFKFFLH VTHEMNIKGF WKDGLHATNL SAIQSFTRPV GVGTQCYELV 600
    RQGTAVGQPV VHTSAMLQVT GEAEYTDDTP TPPNTLHAAL VLSTKAHARI 650
    LSIDASLAKS SPGFAGLFLS KDVPGANHTG PVIHDEEVFA SDVVTCVGQI 700
    VGLVVADTRD NAKAAANKVN IEYSELPAIL SIEEAVKAGS FHPNSKRCLV 750
    KGNVEQCFLS GACDRIIEGK VQVGGQEHFY MEPQSTLVWP VDSGNEIHMI 800
    SSTQAPQKHQ KYVANVLGLP QSRVVCKTKR IGGGFGGKET RSAIFAAAAS 850
    VAAYCLRQPV KLVLDRDIDM MTTGQRHSFL GKYKVGFTDD GKILALDLDV 900
    YNNGGHSHDL SLPVLERAMF HSDNVYDIPN VRVNGQVCFT NFPSNTAFRG 950
    FGGPQAMLIA ENWIQHMATE LKRSPEEIKE LNFQSEGSVL HYGQLLQNCT 1000
    IHSVWDELKV SCNFMEARKA VIDFNNNNRW RKRGIAMVPT KFGISFTTKF 1050
    MNQAGALVQV YTDGTVLVTH GGVEMGQGLH TKVAQVAASS FNIPLSSIFI 1100
    SETSTDKVPN ATPTAASASS DLYGAAVLDA CQQIMARMEP VASRGNHKSF 1150
    AELVLACYLE RIDLSAHGFY ITPDVGFDWV SGKGTPFYYF TYGAAFAEVE 1200
    IDTLTGDFHT RTVDIVMDLG CSINPAIDIG QIEGGFIQGL GWAALEELKW 1250
    GDDNHKWIRP GHLFTCGPGS YKIPSVNDIP LNFKVSLLKG VLNPKVIHSS 1300
    KAVGEPPFFL GSAVLFAIKD AISAARAEEG HFDWFPLDSP ATPERIRMAC 1350
    VDSITKKFAS VYYRPKLSV 1369
    Length:1,369
    Mass (Da):150,227
    Last modified:September 13, 2004 - v1
    Checksum:i470407521B957EA0
    GO

    Sequence cautioni

    The sequence ABF96752.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti1290 – 12901G → D in AK067814. (PubMed:12869764)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC114896 Genomic DNA. Translation: AAT81740.1.
    DP000009 Genomic DNA. Translation: ABF96751.1.
    DP000009 Genomic DNA. Translation: ABF96752.1. Sequence problems.
    AP008209 Genomic DNA. Translation: BAF12334.1.
    CM000140 Genomic DNA. Translation: EEE59305.1.
    AK067814 mRNA. No translation available.
    RefSeqiNP_001050420.1. NM_001056955.1.
    UniGeneiOs.10786.

    Genome annotation databases

    EnsemblPlantsiOS03T0429800-01; OS03T0429800-01; OS03G0429800.
    OS03T0429800-02; OS03T0429800-02; OS03G0429800.
    GeneIDi4333171.
    KEGGiosa:4333171.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC114896 Genomic DNA. Translation: AAT81740.1 .
    DP000009 Genomic DNA. Translation: ABF96751.1 .
    DP000009 Genomic DNA. Translation: ABF96752.1 . Sequence problems.
    AP008209 Genomic DNA. Translation: BAF12334.1 .
    CM000140 Genomic DNA. Translation: EEE59305.1 .
    AK067814 mRNA. No translation available.
    RefSeqi NP_001050420.1. NM_001056955.1.
    UniGenei Os.10786.

    3D structure databases

    ProteinModelPortali Q6AUV1.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi Q6AUV1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi OS03T0429800-01 ; OS03T0429800-01 ; OS03G0429800 .
    OS03T0429800-02 ; OS03T0429800-02 ; OS03G0429800 .
    GeneIDi 4333171.
    KEGGi osa:4333171.

    Organism-specific databases

    Gramenei Q6AUV1.

    Phylogenomic databases

    HOGENOMi HOG000191197.
    KOi K00106.
    OMAi CDETFFA.

    Enzyme and pathway databases

    Reactomei REACT_223073. Vitamins B6 activation to pyridoxal phosphate.

    Family and domain databases

    Gene3Di 1.10.150.120. 1 hit.
    3.10.20.30. 1 hit.
    3.30.365.10. 6 hits.
    3.30.43.10. 1 hit.
    3.30.465.10. 1 hit.
    3.90.1170.50. 1 hit.
    InterProi IPR002888. 2Fe-2S-bd.
    IPR001041. 2Fe-2S_ferredoxin-type.
    IPR006058. 2Fe2S_fd_BS.
    IPR000674. Ald_Oxase/Xan_DH_a/b.
    IPR016208. Ald_Oxase/xanthine_DH.
    IPR008274. AldOxase/xan_DH_Mopterin-bd.
    IPR012675. Beta-grasp_dom.
    IPR005107. CO_DH_flav_C.
    IPR016169. CO_DH_flavot_FAD-bd_sub2.
    IPR016166. FAD-bd_2.
    IPR016167. FAD-bd_2_sub1.
    IPR002346. Mopterin_DH_FAD-bd.
    [Graphical view ]
    Pfami PF01315. Ald_Xan_dh_C. 1 hit.
    PF02738. Ald_Xan_dh_C2. 1 hit.
    PF03450. CO_deh_flav_C. 1 hit.
    PF00941. FAD_binding_5. 1 hit.
    PF00111. Fer2. 1 hit.
    PF01799. Fer2_2. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000127. Xanthine_DH. 1 hit.
    SMARTi SM01008. Ald_Xan_dh_C. 1 hit.
    SM01092. CO_deh_flav_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47741. SSF47741. 1 hit.
    SSF54292. SSF54292. 1 hit.
    SSF54665. SSF54665. 1 hit.
    SSF55447. SSF55447. 1 hit.
    SSF56003. SSF56003. 1 hit.
    SSF56176. SSF56176. 1 hit.
    PROSITEi PS00197. 2FE2S_FER_1. 1 hit.
    PS51085. 2FE2S_FER_2. 1 hit.
    PS51387. FAD_PCMH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species."
      The rice chromosome 3 sequencing consortium
      Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B., Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T., Fadrosh D., Bera J., Weaver B., Jin S.
      , Johri S., Reardon M., Webb K., Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T., Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R., Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J., Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S., Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M., Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M., Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L., O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R., Jin W., Lee H.R., Jiang J., Jackson S.
      Genome Res. 15:1284-1291(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], GENOME REANNOTATION.
      Strain: cv. Nipponbare.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Nipponbare.
    3. "The rice annotation project database (RAP-DB): 2008 update."
      The rice annotation project (RAP)
      Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENOME REANNOTATION.
      Strain: cv. Nipponbare.
    4. "The genomes of Oryza sativa: a history of duplications."
      Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.
      , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.
      PLoS Biol. 3:266-281(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Nipponbare.
    5. "Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice."
      The rice full-length cDNA consortium
      Science 301:376-379(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Nipponbare.

    Entry informationi

    Entry nameiXDH_ORYSJ
    AccessioniPrimary (citable) accession number: Q6AUV1
    Secondary accession number(s): Q10J86
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 16, 2012
    Last sequence update: September 13, 2004
    Last modified: October 1, 2014
    This is version 93 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Oryza sativa (rice)
      Index of Oryza sativa entries and their corresponding gene designations
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3