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F4JLI5

- XDH2_ARATH

UniProt

F4JLI5 - XDH2_ARATH

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Protein
Xanthine dehydrogenase 2
Gene
XDH2, At4g34900, T11I11.140
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at transcript leveli

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi277 – 2848FAD By similarity
Nucleotide bindingi367 – 3715FAD By similarity

GO - Molecular functioni

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

GO - Biological processi

  1. xanthine metabolic process Source: UniProtKB
Complete GO annotation...

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 2
PRO_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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 93872Fe-2S ferredoxin-type
Add
BLAST
Domaini249 – 434186FAD-binding PCMH-type
Add
BLAST

Sequence similaritiesi

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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti401 – 4011V → A in AAR99079. 1 Publication

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...

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 28 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

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