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F4JLI5

- XDH2_ARATH

UniProt

F4JLI5 - XDH2_ARATH

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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

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
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 2PRO_0000417458Add
BLAST

Proteomic databases

PRIDEiF4JLI5.

Expressioni

Tissue specificityi

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

Gene expression databases

ExpressionAtlasiF4JLI5. baseline.

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.
InParanoidiF4JLI5.
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

        10         20         30         40         50
MEQNEFMEAI MYVNGVRRVL PDGLAHMTLL EYLRDLGLTG TKLGCGEGGC
60 70 80 90 100
GSCTVMVSSY DRESKTCVHY AVNACLAPLY SVEGMHVISI EGVGHRKLGL
110 120 130 140 150
HPLQESLASS HGSQCGFCTP GFVMSMYALL RSSKNSPSEE EIEECLAGNL
160 170 180 190 200
CRCTGYRPII DAFRVFAKSD DALYSGLSSL SLQDGSNICP STGKPCSCGS
210 220 230 240 250
KTTSEAATCN EDRFQSISYS DIDGAKYTDK ELIFPPELLL RKLAPLKLGG
260 270 280 290 300
NEGITWYRPV SLQNLLELKA NFPDAKLLVG NTEVGIEMRL KRLQYPVLIS
310 320 330 340 350
AAQVPELNAL NVNDNGIEVG SALRLSELLR LFRKVVKERP AHETSACKAF
360 370 380 390 400
IEQLKWFAGT QIRNVACIGG NICTASPISD LNPLWMASRA EFRIINCNGD
410 420 430 440 450
VRSIPAKDFF LGYRKVDMGS NEILLSVFLP WTRPLEYVKE FKQAHRRDDD
460 470 480 490 500
IAIVNGGMRV FLEEKGQQLF VSDASIVYGG VAPLSLRARN TEELLIGKNW
510 520 530 540 550
NKCLLQDALK VIQSDVLIKE GAPGGMVEFR KSLTLSFFFK FFLWVTHHVN
560 570 580 590 600
NVNPTIETFP PSHMSAVQLV PRFSRIGKQD YETVKQGTSV GLPEVHLSAR
610 620 630 640 650
MQVTGEAEYT DDTPLPPCTL HAALVLSKVP HARILSVDDS AAKSSSGFVG
660 670 680 690 700
LFLAKDVPGN NMIGPIVADE ELFATDVVTC VGQVIGVLVA DTHENAKTAA
710 720 730 740 750
RKVDVRYQEL PAILSIKEAI NAKSFHPNTE RRLRKGDVEL CFQSGQCDRI
760 770 780 790 800
IEGEVQMGGQ EHFYLEPNGS LVWTIDGGNE VHMISSTQAP QQHQKYVSHV
810 820 830 840 850
LGLPMSKVVC KTKRLGGGFG GKETRSAFIA AAASVPSYLL NRPVKLILDR
860 870 880 890 900
DVDMMITGHR HSFVGKYKVG FTNEGKILAL DLEIYNNGGN SMDLSLSNLE
910 920 930 940 950
RAMFHSDNVY EIPHVRIVGN VCFTNFPSNT AFRGFGGPQG MLITENWIQR
960 970 980 990 1000
IAAELDKIPE EIKEMNFQVE GSITHYFQSL QHCTLHQLWK ELKVSSNFLK
1010 1020 1030 1040 1050
TRREADEFNS HNRWKKRGVA MVPTKFGISF TTKFMNQAGA LVHVYTDGTV
1060 1070 1080 1090 1100
LVTHGGVEMG QGLHTKVAQV AATAFNILLS SVFVSETSTD KVPNASPTAA
1110 1120 1130 1140 1150
SASSDMYGAA VLDACEQIIA RMEPVASKHN FNTFSELASA CYFQRIDLSA
1160 1170 1180 1190 1200
HGFHIVPELE FDWVSGKGNA YRYYTYGAAF AEVEIDTLTG DFHTRKADIM
1210 1220 1230 1240 1250
LDLGYSLNPT IDIGQIEGAF VQGLGWVALE ELKWGDAAHK WIKPGSLLTC
1260 1270 1280 1290 1300
GPGSYKIPSI NDMPFQLNVS LLKGNPNAKA IHSSKAVGEP PFFLAASAFF
1310 1320 1330 1340 1350
AIKEAIKAAR SEVGLTNWFP LETPATPERI RMACFDEFSA PFANSDFCPK

LSV
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.
InParanoidi F4JLI5.
KOi K00106.
OMAi MACETIL.

Enzyme and pathway databases

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

Gene expression databases

ExpressionAtlasi F4JLI5. baseline.

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: October 29, 2014
This is version 30 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