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Q6AUV1

- XDH_ORYSJ

UniProt

Q6AUV1 - XDH_ORYSJ

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Protein

Xanthine dehydrogenase

Gene

XDH

Organism
Oryza sativa subsp. japonica (Rice)
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 (By similarity).By similarity

Catalytic activityi

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

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)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
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_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.

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.
InParanoidiQ6AUV1.
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

        10         20         30         40         50
MGSLTRAEEE ETAAAEEWSG EAVVYVNGVR RVLPDGLAHL TLLQYLRDIG
60 70 80 90 100
LPGTKLGCGE GGCGACTVMV SCYDQTTKKT QHFAINACLA PLYSVEGMHI
110 120 130 140 150
ITVEGIGNRQ RGLHPIQERL AMAHGSQCGF CTPGFVMSMY ALLRSSEQPP
160 170 180 190 200
TEEQIEDSLA GNLCRCTGYR PIIDAFRVFS KRDDLLYNNS SLKNADGRPI
210 220 230 240 250
CPSTGKPCSC GDQKDINGSE SSLLTPTKSY SPCSYNEIDG NAYSEKELIF
260 270 280 290 300
PPELQLRKVT SLKLNGFNGI RWYRPLKLKQ VLHLKACYPN AKLIIGNSEV
310 320 330 340 350
GVETKFKNAQ YKVLISVTHV PELHTLKVKE DGIHIGSSVR LAQLQNFLRK
360 370 380 390 400
VILERDSHEI SSCEAILRQL KWFAGTQIRN VASVGGNICT ASPISDLNPL
410 420 430 440 450
WMATGATFEI IDVNNNIRTI PAKDFFLGYR KVDLKPDEIL LSVILPWTRP
460 470 480 490 500
FEFVKEFKQA HRREDDIALV NAGMRVYIRK VEGDWIISDV SIIYGGVAAV
510 520 530 540 550
SHRASKTETF LTGKKWDYGL LDKTFDLLKE DVVLAENAPG GMVEFRSSLT
560 570 580 590 600
LSFFFKFFLH VTHEMNIKGF WKDGLHATNL SAIQSFTRPV GVGTQCYELV
610 620 630 640 650
RQGTAVGQPV VHTSAMLQVT GEAEYTDDTP TPPNTLHAAL VLSTKAHARI
660 670 680 690 700
LSIDASLAKS SPGFAGLFLS KDVPGANHTG PVIHDEEVFA SDVVTCVGQI
710 720 730 740 750
VGLVVADTRD NAKAAANKVN IEYSELPAIL SIEEAVKAGS FHPNSKRCLV
760 770 780 790 800
KGNVEQCFLS GACDRIIEGK VQVGGQEHFY MEPQSTLVWP VDSGNEIHMI
810 820 830 840 850
SSTQAPQKHQ KYVANVLGLP QSRVVCKTKR IGGGFGGKET RSAIFAAAAS
860 870 880 890 900
VAAYCLRQPV KLVLDRDIDM MTTGQRHSFL GKYKVGFTDD GKILALDLDV
910 920 930 940 950
YNNGGHSHDL SLPVLERAMF HSDNVYDIPN VRVNGQVCFT NFPSNTAFRG
960 970 980 990 1000
FGGPQAMLIA ENWIQHMATE LKRSPEEIKE LNFQSEGSVL HYGQLLQNCT
1010 1020 1030 1040 1050
IHSVWDELKV SCNFMEARKA VIDFNNNNRW RKRGIAMVPT KFGISFTTKF
1060 1070 1080 1090 1100
MNQAGALVQV YTDGTVLVTH GGVEMGQGLH TKVAQVAASS FNIPLSSIFI
1110 1120 1130 1140 1150
SETSTDKVPN ATPTAASASS DLYGAAVLDA CQQIMARMEP VASRGNHKSF
1160 1170 1180 1190 1200
AELVLACYLE RIDLSAHGFY ITPDVGFDWV SGKGTPFYYF TYGAAFAEVE
1210 1220 1230 1240 1250
IDTLTGDFHT RTVDIVMDLG CSINPAIDIG QIEGGFIQGL GWAALEELKW
1260 1270 1280 1290 1300
GDDNHKWIRP GHLFTCGPGS YKIPSVNDIP LNFKVSLLKG VLNPKVIHSS
1310 1320 1330 1340 1350
KAVGEPPFFL GSAVLFAIKD AISAARAEEG HFDWFPLDSP ATPERIRMAC
1360
VDSITKKFAS VYYRPKLSV
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. Curated

Experimental Info

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

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.
InParanoidi Q6AUV1.
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

« Hide 'large scale' publications
  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].
    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: November 26, 2014
This is version 95 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