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Protein

Xanthine dehydrogenase 2

Gene

XDH2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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.By similarity
Hypoxanthine + NAD+ + H2O = xanthine + NADH.By similarity

Cofactori

Protein has several cofactor binding sites:
  • [2Fe-2S] clusterBy similarityNote: Binds 2 [2Fe-2S] clusters.By similarity
  • FADBy similarity
  • Mo-molybdopterinBy similarityNote: Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi45Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation1
Metal bindingi50Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation1
Metal bindingi53Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation1
Metal bindingi75Iron-sulfur (2Fe-2S) 1PROSITE-ProRule annotation1
Metal bindingi115Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation1
Metal bindingi118Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation1
Metal bindingi151Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation1
Metal bindingi153Iron-sulfur (2Fe-2S) 2PROSITE-ProRule annotation1
Binding sitei357FADBy similarity1
Binding sitei380FADBy similarity1
Binding sitei424FAD; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei442FADBy similarity1
Metal bindingi788MolybdenumBy similarity1
Metal bindingi819Molybdenum; via carbonyl oxygenBy similarity1
Binding sitei823SubstrateBy similarity1
Binding sitei901SubstrateBy similarity1
Metal bindingi933Molybdenum; via amide nitrogenBy similarity1
Binding sitei935SubstrateBy similarity1
Binding sitei1031SubstrateBy similarity1
Metal bindingi1100Molybdenum; via amide nitrogenBy similarity1
Active sitei1289Proton acceptorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi277 – 284FADBy similarity8
Nucleotide bindingi367 – 371FADBy similarity5

GO - Molecular functioni

GO - Biological processi

  • 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

ReactomeiR-ATH-74259. Purine catabolism.
R-ATH-964975. Vitamins B6 activation to pyridoxal phosphate.

Names & Taxonomyi

Protein namesi
Recommended name:
Xanthine dehydrogenase 2 (EC:1.17.1.4By similarity)
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
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G34900.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004174581 – 1353Xanthine dehydrogenase 2Add BLAST1353

Proteomic databases

PaxDbiF4JLI5.

Expressioni

Tissue specificityi

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

Gene expression databases

GenevisibleiF4JLI5. AT.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi3702.AT4G34900.1.

Structurei

3D structure databases

ProteinModelPortaliF4JLI5.
SMRiF4JLI5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini7 – 932Fe-2S ferredoxin-typePROSITE-ProRule annotationAdd BLAST87
Domaini249 – 434FAD-binding PCMH-typePROSITE-ProRule annotationAdd BLAST186

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

eggNOGiKOG0430. Eukaryota.
COG4630. LUCA.
COG4631. LUCA.
HOGENOMiHOG000191197.
InParanoidiF4JLI5.
KOiK00106.
OMAiMIRHIAS.
OrthoDBiEOG093600B8.

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti401V → A in AAR99079 (PubMed:14726515).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_119656.3.
UniGeneiAt.31462.

Genome annotation databases

EnsemblPlantsiAT4G34900.1; AT4G34900.1; AT4G34900.
GeneIDi829642.
GrameneiAT4G34900.1; AT4G34900.1; AT4G34900.
KEGGiath:AT4G34900.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_119656.3.
UniGeneiAt.31462.

3D structure databases

ProteinModelPortaliF4JLI5.
SMRiF4JLI5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT4G34900.1.

Proteomic databases

PaxDbiF4JLI5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G34900.1; AT4G34900.1; AT4G34900.
GeneIDi829642.
GrameneiAT4G34900.1; AT4G34900.1; AT4G34900.
KEGGiath:AT4G34900.

Organism-specific databases

TAIRiAT4G34900.

Phylogenomic databases

eggNOGiKOG0430. Eukaryota.
COG4630. LUCA.
COG4631. LUCA.
HOGENOMiHOG000191197.
InParanoidiF4JLI5.
KOiK00106.
OMAiMIRHIAS.
OrthoDBiEOG093600B8.

Enzyme and pathway databases

ReactomeiR-ATH-74259. Purine catabolism.
R-ATH-964975. Vitamins B6 activation to pyridoxal phosphate.

Miscellaneous databases

PROiF4JLI5.

Gene expression databases

GenevisibleiF4JLI5. AT.

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]
ProtoNetiSearch...

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: November 30, 2016
This is version 46 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.