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F4JLI5

- XDH2_ARATH

UniProt

F4JLI5 - XDH2_ARATH

Protein

Xanthine dehydrogenase 2

Gene

XDH2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 29 (01 Oct 2014)
      Sequence version 1 (28 Jun 2011)
      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. Regulates the level of ureides and plays a role during plant growth and development and senescence.1 Publication

    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 bindingi45 – 451Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation
    Metal bindingi50 – 501Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation
    Metal bindingi53 – 531Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation
    Metal bindingi75 – 751Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation
    Metal bindingi115 – 1151Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation
    Metal bindingi118 – 1181Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation
    Metal bindingi151 – 1511Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation
    Metal bindingi153 – 1531Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation
    Binding sitei357 – 3571FADBy similarity
    Binding sitei380 – 3801FADBy similarity
    Binding sitei424 – 4241FAD; via amide nitrogen and carbonyl oxygenBy similarity
    Binding sitei442 – 4421FADBy similarity
    Metal bindingi788 – 7881MolybdenumBy similarity
    Metal bindingi819 – 8191Molybdenum; via carbonyl oxygenBy similarity
    Binding sitei823 – 8231SubstrateBy similarity
    Binding sitei901 – 9011SubstrateBy similarity
    Metal bindingi933 – 9331Molybdenum; via amide nitrogenBy similarity
    Binding sitei935 – 9351SubstrateBy similarity
    Binding sitei1031 – 10311SubstrateBy similarity
    Metal bindingi1100 – 11001Molybdenum; via amide nitrogenBy similarity
    Active sitei1289 – 12891Proton acceptorBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi277 – 2848FADBy similarity
    Nucleotide bindingi367 – 3715FADBy 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. xanthine metabolic process Source: UniProtKB

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

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

    Enzyme and pathway databases

    ReactomeiREACT_187833. Vitamins B6 activation to pyridoxal phosphate.
    REACT_219858. Purine catabolism.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Xanthine dehydrogenase 2 (EC:1.17.1.4)
    Short name:
    AtXDH2
    Gene namesi
    Name:XDH2
    Ordered Locus Names:At4g34900
    ORF Names:T11I11.140
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 4

    Organism-specific databases

    TAIRiAT4G34900.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 13531353Xanthine dehydrogenase 2PRO_0000417458Add
    BLAST

    Proteomic databases

    PRIDEiF4JLI5.

    Expressioni

    Tissue specificityi

    Expressed in roots, leaves, stems, flowers and siliques.

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    STRINGi3702.AT4G34900.1-P.

    Structurei

    3D structure databases

    ProteinModelPortaliF4JLI5.
    SMRiF4JLI5. Positions 8-168, 230-545, 589-1339.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini7 – 93872Fe-2S ferredoxin-typePROSITE-ProRule annotationAdd
    BLAST
    Domaini249 – 434186FAD-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.
    OMAiMACETIL.

    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.

    F4JLI5-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEQNEFMEAI MYVNGVRRVL PDGLAHMTLL EYLRDLGLTG TKLGCGEGGC     50
    GSCTVMVSSY DRESKTCVHY AVNACLAPLY SVEGMHVISI EGVGHRKLGL 100
    HPLQESLASS HGSQCGFCTP GFVMSMYALL RSSKNSPSEE EIEECLAGNL 150
    CRCTGYRPII DAFRVFAKSD DALYSGLSSL SLQDGSNICP STGKPCSCGS 200
    KTTSEAATCN EDRFQSISYS DIDGAKYTDK ELIFPPELLL RKLAPLKLGG 250
    NEGITWYRPV SLQNLLELKA NFPDAKLLVG NTEVGIEMRL KRLQYPVLIS 300
    AAQVPELNAL NVNDNGIEVG SALRLSELLR LFRKVVKERP AHETSACKAF 350
    IEQLKWFAGT QIRNVACIGG NICTASPISD LNPLWMASRA EFRIINCNGD 400
    VRSIPAKDFF LGYRKVDMGS NEILLSVFLP WTRPLEYVKE FKQAHRRDDD 450
    IAIVNGGMRV FLEEKGQQLF VSDASIVYGG VAPLSLRARN TEELLIGKNW 500
    NKCLLQDALK VIQSDVLIKE GAPGGMVEFR KSLTLSFFFK FFLWVTHHVN 550
    NVNPTIETFP PSHMSAVQLV PRFSRIGKQD YETVKQGTSV GLPEVHLSAR 600
    MQVTGEAEYT DDTPLPPCTL HAALVLSKVP HARILSVDDS AAKSSSGFVG 650
    LFLAKDVPGN NMIGPIVADE ELFATDVVTC VGQVIGVLVA DTHENAKTAA 700
    RKVDVRYQEL PAILSIKEAI NAKSFHPNTE RRLRKGDVEL CFQSGQCDRI 750
    IEGEVQMGGQ EHFYLEPNGS LVWTIDGGNE VHMISSTQAP QQHQKYVSHV 800
    LGLPMSKVVC KTKRLGGGFG GKETRSAFIA AAASVPSYLL NRPVKLILDR 850
    DVDMMITGHR HSFVGKYKVG FTNEGKILAL DLEIYNNGGN SMDLSLSNLE 900
    RAMFHSDNVY EIPHVRIVGN VCFTNFPSNT AFRGFGGPQG MLITENWIQR 950
    IAAELDKIPE EIKEMNFQVE GSITHYFQSL QHCTLHQLWK ELKVSSNFLK 1000
    TRREADEFNS HNRWKKRGVA MVPTKFGISF TTKFMNQAGA LVHVYTDGTV 1050
    LVTHGGVEMG QGLHTKVAQV AATAFNILLS SVFVSETSTD KVPNASPTAA 1100
    SASSDMYGAA VLDACEQIIA RMEPVASKHN FNTFSELASA CYFQRIDLSA 1150
    HGFHIVPELE FDWVSGKGNA YRYYTYGAAF AEVEIDTLTG DFHTRKADIM 1200
    LDLGYSLNPT IDIGQIEGAF VQGLGWVALE ELKWGDAAHK WIKPGSLLTC 1250
    GPGSYKIPSI NDMPFQLNVS LLKGNPNAKA IHSSKAVGEP PFFLAASAFF 1300
    AIKEAIKAAR SEVGLTNWFP LETPATPERI RMACFDEFSA PFANSDFCPK 1350
    LSV 1353
    Length:1,353
    Mass (Da):148,762
    Last modified:June 28, 2011 - v1
    Checksum:iFC1AD990E687DD3A
    GO

    Sequence cautioni

    The sequence CAB45451.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence CAB80207.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti401 – 4011V → A in AAR99079. (PubMed:14726515)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY518202 mRNA. Translation: AAR99079.1.
    AL079347 Genomic DNA. Translation: CAB45451.1. Sequence problems.
    AL161586 Genomic DNA. Translation: CAB80207.1. Sequence problems.
    CP002687 Genomic DNA. Translation: AEE86435.1.
    PIRiT10236.
    RefSeqiNP_195216.2. NM_119656.2.
    UniGeneiAt.31462.

    Genome annotation databases

    EnsemblPlantsiAT4G34900.1; AT4G34900.1; AT4G34900.
    GeneIDi829642.
    KEGGiath:AT4G34900.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY518202 mRNA. Translation: AAR99079.1 .
    AL079347 Genomic DNA. Translation: CAB45451.1 . Sequence problems.
    AL161586 Genomic DNA. Translation: CAB80207.1 . Sequence problems.
    CP002687 Genomic DNA. Translation: AEE86435.1 .
    PIRi T10236.
    RefSeqi NP_195216.2. NM_119656.2.
    UniGenei At.31462.

    3D structure databases

    ProteinModelPortali F4JLI5.
    SMRi F4JLI5. Positions 8-168, 230-545, 589-1339.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT4G34900.1-P.

    Proteomic databases

    PRIDEi F4JLI5.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G34900.1 ; AT4G34900.1 ; AT4G34900 .
    GeneIDi 829642.
    KEGGi ath:AT4G34900.

    Organism-specific databases

    TAIRi AT4G34900.

    Phylogenomic databases

    HOGENOMi HOG000191197.
    KOi K00106.
    OMAi MACETIL.

    Enzyme and pathway databases

    Reactomei REACT_187833. Vitamins B6 activation to pyridoxal phosphate.
    REACT_219858. Purine catabolism.

    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. "Tandem orientation of duplicated xanthine dehydrogenase genes from Arabidopsis thaliana: differential gene expression and enzyme activities."
      Hesberg C., Haensch R., Mendel R.R., Bittner F.
      J. Biol. Chem. 279:13547-13554(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
      Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
      , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
      Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "The RNAi-mediated silencing of xanthine dehydrogenase impairs growth and fertility and accelerates leaf senescence in transgenic Arabidopsis plants."
      Nakagawa A., Sakamoto S., Takahashi M., Morikawa H., Sakamoto A.
      Plant Cell Physiol. 48:1484-1495(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiXDH2_ARATH
    AccessioniPrimary (citable) accession number: F4JLI5
    Secondary accession number(s): Q6R2R5, Q9SW45
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 16, 2012
    Last sequence update: June 28, 2011
    Last modified: October 1, 2014
    This is version 29 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Plants silencing simultaneously XDH1 and XDH2 show reduced growth, impaired silique development, increased seed sterility, precocious senescence of mature leaves and overaccumulation of xanthine.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3