XDH_ORYSJ
ID XDH_ORYSJ Reviewed; 1369 AA.
AC Q6AUV1; A0A0P0VZ09; Q10J86;
DT 16-MAY-2012, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2004, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Xanthine dehydrogenase;
DE EC=1.17.1.4 {ECO:0000250|UniProtKB:Q8GUQ8};
GN Name=XDH; OrderedLocusNames=Os03g0429800, LOC_Os03g31550;
GN ORFNames=OsJ_11360, OSJNBa0091B22.11;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Key enzyme involved in purine catabolism. Catalyzes the
CC oxidation of hypoxanthine to xanthine and the oxidation of xanthine to
CC urate. {ECO:0000250|UniProtKB:Q8GUQ8}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NAD(+) + xanthine = H(+) + NADH + urate;
CC Xref=Rhea:RHEA:16669, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17712, ChEBI:CHEBI:17775, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.17.1.4;
CC Evidence={ECO:0000250|UniProtKB:Q8GUQ8};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + hypoxanthine + NAD(+) = H(+) + NADH + xanthine;
CC Xref=Rhea:RHEA:24670, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17368, ChEBI:CHEBI:17712, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.17.1.4;
CC Evidence={ECO:0000250|UniProtKB:Q8GUQ8};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135; Evidence={ECO:0000250};
CC Note=Binds 2 [2Fe-2S] clusters. {ECO:0000250};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
CC -!- COFACTOR:
CC Name=Mo-molybdopterin; Xref=ChEBI:CHEBI:71302; Evidence={ECO:0000250};
CC Note=Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit.
CC {ECO:0000250};
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the xanthine dehydrogenase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABF96752.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC114896; AAT81740.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF96751.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF96752.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008209; BAF12334.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS84804.1; -; Genomic_DNA.
DR EMBL; CM000140; EEE59305.1; -; Genomic_DNA.
DR EMBL; AK067814; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015630851.1; XM_015775365.1.
DR RefSeq; XP_015630852.1; XM_015775366.1.
DR AlphaFoldDB; Q6AUV1; -.
DR SMR; Q6AUV1; -.
DR STRING; 4530.OS03T0429800-01; -.
DR PaxDb; Q6AUV1; -.
DR PRIDE; Q6AUV1; -.
DR EnsemblPlants; Os03t0429800-01; Os03t0429800-01; Os03g0429800.
DR EnsemblPlants; Os03t0429800-02; Os03t0429800-02; Os03g0429800.
DR GeneID; 4333171; -.
DR Gramene; Os03t0429800-01; Os03t0429800-01; Os03g0429800.
DR Gramene; Os03t0429800-02; Os03t0429800-02; Os03g0429800.
DR KEGG; osa:4333171; -.
DR eggNOG; KOG0430; Eukaryota.
DR HOGENOM; CLU_001681_1_2_1; -.
DR InParanoid; Q6AUV1; -.
DR OMA; DIGYVWG; -.
DR OrthoDB; 48717at2759; -.
DR PlantReactome; R-OSA-1119407; Ureide biosynthesis.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR ExpressionAtlas; Q6AUV1; baseline and differential.
DR Genevisible; Q6AUV1; OS.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0071949; F:FAD binding; IEA:InterPro.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0004854; F:xanthine dehydrogenase activity; IEA:UniProtKB-EC.
DR Gene3D; 3.10.20.30; -; 1.
DR Gene3D; 3.30.43.10; -; 1.
DR Gene3D; 3.30.465.10; -; 1.
DR InterPro; IPR002888; 2Fe-2S-bd.
DR InterPro; IPR036884; 2Fe-2S-bd_dom_sf.
DR InterPro; IPR036010; 2Fe-2S_ferredoxin-like_sf.
DR InterPro; IPR001041; 2Fe-2S_ferredoxin-type.
DR InterPro; IPR006058; 2Fe2S_fd_BS.
DR InterPro; IPR000674; Ald_Oxase/Xan_DH_a/b.
DR InterPro; IPR036856; Ald_Oxase/Xan_DH_a/b_sf.
DR InterPro; IPR016208; Ald_Oxase/xanthine_DH.
DR InterPro; IPR008274; AldOxase/xan_DH_Mopterin-bd.
DR InterPro; IPR037165; AldOxase/xan_DH_Mopterin-bd_sf.
DR InterPro; IPR012675; Beta-grasp_dom_sf.
DR InterPro; IPR005107; CO_DH_flav_C.
DR InterPro; IPR036683; CO_DH_flav_C_dom_sf.
DR InterPro; IPR016166; FAD-bd_PCMH.
DR InterPro; IPR036318; FAD-bd_PCMH-like_sf.
DR InterPro; IPR016167; FAD-bd_PCMH_sub1.
DR InterPro; IPR016169; FAD-bd_PCMH_sub2.
DR InterPro; IPR002346; Mopterin_DH_FAD-bd.
DR PANTHER; PTHR11908; PTHR11908; 1.
DR Pfam; PF01315; Ald_Xan_dh_C; 1.
DR Pfam; PF02738; Ald_Xan_dh_C2; 1.
DR Pfam; PF03450; CO_deh_flav_C; 1.
DR Pfam; PF00941; FAD_binding_5; 1.
DR Pfam; PF00111; Fer2; 1.
DR Pfam; PF01799; Fer2_2; 1.
DR PIRSF; PIRSF000127; Xanthine_DH; 1.
DR SMART; SM01008; Ald_Xan_dh_C; 1.
DR SMART; SM01092; CO_deh_flav_C; 1.
DR SUPFAM; SSF47741; SSF47741; 1.
DR SUPFAM; SSF54292; SSF54292; 1.
DR SUPFAM; SSF54665; SSF54665; 1.
DR SUPFAM; SSF55447; SSF55447; 1.
DR SUPFAM; SSF56003; SSF56003; 1.
DR SUPFAM; SSF56176; SSF56176; 1.
DR PROSITE; PS00197; 2FE2S_FER_1; 1.
DR PROSITE; PS51085; 2FE2S_FER_2; 1.
DR PROSITE; PS51387; FAD_PCMH; 1.
PE 2: Evidence at transcript level;
KW 2Fe-2S; FAD; Flavoprotein; Iron; Iron-sulfur; Metal-binding; Molybdenum;
KW NAD; Oxidoreductase; Reference proteome.
FT CHAIN 1..1369
FT /note="Xanthine dehydrogenase"
FT /id="PRO_0000417459"
FT DOMAIN 20..106
FT /note="2Fe-2S ferredoxin-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT DOMAIN 265..450
FT /note="FAD-binding PCMH-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00718"
FT ACT_SITE 1305
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 58
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 63
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 66
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 88
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 128
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 131
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 164
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 166
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 293..300
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 373
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 383..387
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 396
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 440
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 458
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 804
FT /ligand="Mo-molybdopterin"
FT /ligand_id="ChEBI:CHEBI:71302"
FT /ligand_part="Mo"
FT /ligand_part_id="ChEBI:CHEBI:28685"
FT /evidence="ECO:0000250"
FT BINDING 835
FT /ligand="Mo-molybdopterin"
FT /ligand_id="ChEBI:CHEBI:71302"
FT /ligand_part="Mo"
FT /ligand_part_id="ChEBI:CHEBI:28685"
FT /evidence="ECO:0000250"
FT BINDING 839
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 917
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 949
FT /ligand="Mo-molybdopterin"
FT /ligand_id="ChEBI:CHEBI:71302"
FT /ligand_part="Mo"
FT /ligand_part_id="ChEBI:CHEBI:28685"
FT /evidence="ECO:0000250"
FT BINDING 951
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 1047
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 1116
FT /ligand="Mo-molybdopterin"
FT /ligand_id="ChEBI:CHEBI:71302"
FT /ligand_part="Mo"
FT /ligand_part_id="ChEBI:CHEBI:28685"
FT /evidence="ECO:0000250"
FT CONFLICT 1290
FT /note="G -> D (in Ref. 6; AK067814)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1369 AA; 150227 MW; 470407521B957EA0 CRC64;
MGSLTRAEEE ETAAAEEWSG EAVVYVNGVR RVLPDGLAHL TLLQYLRDIG LPGTKLGCGE
GGCGACTVMV SCYDQTTKKT QHFAINACLA PLYSVEGMHI ITVEGIGNRQ RGLHPIQERL
AMAHGSQCGF CTPGFVMSMY ALLRSSEQPP TEEQIEDSLA GNLCRCTGYR PIIDAFRVFS
KRDDLLYNNS SLKNADGRPI CPSTGKPCSC GDQKDINGSE SSLLTPTKSY SPCSYNEIDG
NAYSEKELIF PPELQLRKVT SLKLNGFNGI RWYRPLKLKQ VLHLKACYPN AKLIIGNSEV
GVETKFKNAQ YKVLISVTHV PELHTLKVKE DGIHIGSSVR LAQLQNFLRK VILERDSHEI
SSCEAILRQL KWFAGTQIRN VASVGGNICT ASPISDLNPL WMATGATFEI IDVNNNIRTI
PAKDFFLGYR KVDLKPDEIL LSVILPWTRP FEFVKEFKQA HRREDDIALV NAGMRVYIRK
VEGDWIISDV SIIYGGVAAV SHRASKTETF LTGKKWDYGL LDKTFDLLKE DVVLAENAPG
GMVEFRSSLT LSFFFKFFLH VTHEMNIKGF WKDGLHATNL SAIQSFTRPV GVGTQCYELV
RQGTAVGQPV VHTSAMLQVT GEAEYTDDTP TPPNTLHAAL VLSTKAHARI LSIDASLAKS
SPGFAGLFLS KDVPGANHTG PVIHDEEVFA SDVVTCVGQI VGLVVADTRD NAKAAANKVN
IEYSELPAIL SIEEAVKAGS FHPNSKRCLV KGNVEQCFLS GACDRIIEGK VQVGGQEHFY
MEPQSTLVWP VDSGNEIHMI SSTQAPQKHQ KYVANVLGLP QSRVVCKTKR IGGGFGGKET
RSAIFAAAAS VAAYCLRQPV KLVLDRDIDM MTTGQRHSFL GKYKVGFTDD GKILALDLDV
YNNGGHSHDL SLPVLERAMF HSDNVYDIPN VRVNGQVCFT NFPSNTAFRG FGGPQAMLIA
ENWIQHMATE LKRSPEEIKE LNFQSEGSVL HYGQLLQNCT IHSVWDELKV SCNFMEARKA
VIDFNNNNRW RKRGIAMVPT KFGISFTTKF MNQAGALVQV YTDGTVLVTH GGVEMGQGLH
TKVAQVAASS FNIPLSSIFI SETSTDKVPN ATPTAASASS DLYGAAVLDA CQQIMARMEP
VASRGNHKSF AELVLACYLE RIDLSAHGFY ITPDVGFDWV SGKGTPFYYF TYGAAFAEVE
IDTLTGDFHT RTVDIVMDLG CSINPAIDIG QIEGGFIQGL GWAALEELKW GDDNHKWIRP
GHLFTCGPGS YKIPSVNDIP LNFKVSLLKG VLNPKVIHSS KAVGEPPFFL GSAVLFAIKD
AISAARAEEG HFDWFPLDSP ATPERIRMAC VDSITKKFAS VYYRPKLSV
