Q6AUV1 (XDH_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Xanthine dehydrogenase
EC=1.17.1.4

Gene names

Name:	XDH
Ordered Locus Names:	Os03g0429800, LOC_Os03g31550
ORF Names:	OsJ_11360, OSJNBa0091B22.11

Organism

Oryza sativa subsp. japonica (Rice) [Reference proteome]

Taxonomic identifier

39947 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › Liliopsida › commelinids › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza › Oryza sativa

Protein attributes

Sequence length	1369 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Key enzyme involved in purine catabolism. Catalyzes the oxidation of hypoxanthine to xanthine and the oxidation of xanthine to urate By similarity.
Catalytic activity	Xanthine + NAD+ + H2O = urate + NADH. Hypoxanthine + NAD+ + H2O = xanthine + NADH.
Cofactor	Binds 2 2Fe-2S clusters By similarity. FAD By similarity. Binds 1 molybdenum ion (molybdopterin) per subunit By similarity.
Subunit structure	Homodimer By similarity.
Sequence similarities	Belongs to the xanthine dehydrogenase family. Contains 1 2Fe-2S ferredoxin-type domain. Contains 1 FAD-binding PCMH-type domain.
Sequence caution	The sequence ABF96752.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Ligand	2Fe-2S FAD Flavoprotein Iron Iron-sulfur Metal-binding Molybdenum NAD
Molecular function	Oxidoreductase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	response to reactive oxygen species Inferred from electronic annotation. Source: EnsemblPlants/Gramene response to water deprivation Inferred from electronic annotation. Source: EnsemblPlants/Gramene superoxide anion generation Inferred from electronic annotation. Source: EnsemblPlants/Gramene xanthine metabolic process Inferred from electronic annotation. Source: EnsemblPlants/Gramene
Molecular_function	2 iron, 2 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW UDP-N-acetylmuramate dehydrogenase activity Inferred from electronic annotation. Source: InterPro electron carrier activity Inferred from electronic annotation. Source: InterPro flavin adenine dinucleotide binding Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: InterPro xanthine dehydrogenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1369	1369	Xanthine dehydrogenase		PRO_0000417459
Regions
	Domain	20 – 106	87	2Fe-2S ferredoxin-type
	Domain	265 – 450	186	FAD-binding PCMH-type
	Nucleotide binding	293 – 300	8	FAD By similarity
	Nucleotide binding	383 – 387	5	FAD By similarity
Sites
	Active site	1305	1	Proton acceptor By similarity
	Metal binding	58	1	Iron-sulfur (2Fe-2S) 1 By similarity
	Metal binding	63	1	Iron-sulfur (2Fe-2S) 1 By similarity
	Metal binding	66	1	Iron-sulfur (2Fe-2S) 1 By similarity
	Metal binding	88	1	Iron-sulfur (2Fe-2S) 1 By similarity
	Metal binding	128	1	Iron-sulfur (2Fe-2S) 2 By similarity
	Metal binding	131	1	Iron-sulfur (2Fe-2S) 2 By similarity
	Metal binding	164	1	Iron-sulfur (2Fe-2S) 2 By similarity
	Metal binding	166	1	Iron-sulfur (2Fe-2S) 2 By similarity
	Metal binding	804	1	Molybdenum By similarity
	Metal binding	835	1	Molybdenum; via carbonyl oxygen By similarity
	Metal binding	949	1	Molybdenum; via amide nitrogen By similarity
	Metal binding	1116	1	Molybdenum; via amide nitrogen By similarity
	Binding site	373	1	FAD By similarity
	Binding site	396	1	FAD By similarity
	Binding site	440	1	FAD; via amide nitrogen and carbonyl oxygen By similarity
	Binding site	458	1	FAD By similarity
	Binding site	839	1	Substrate By similarity
	Binding site	917	1	Substrate By similarity
	Binding site	951	1	Substrate By similarity
	Binding site	1047	1	Substrate By similarity
Experimental info
	Sequence conflict	1290	1	G → D in AK067814. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Q6AUV1 [UniParc]. Last modified September 13, 2004. Version 1. Checksum: 470407521B957EA0	FASTA	1,369	150,227
	10 20 30 40 50 60 MGSLTRAEEE ETAAAEEWSG EAVVYVNGVR RVLPDGLAHL TLLQYLRDIG LPGTKLGCGE 70 80 90 100 110 120 GGCGACTVMV SCYDQTTKKT QHFAINACLA PLYSVEGMHI ITVEGIGNRQ RGLHPIQERL 130 140 150 160 170 180 AMAHGSQCGF CTPGFVMSMY ALLRSSEQPP TEEQIEDSLA GNLCRCTGYR PIIDAFRVFS 190 200 210 220 230 240 KRDDLLYNNS SLKNADGRPI CPSTGKPCSC GDQKDINGSE SSLLTPTKSY SPCSYNEIDG 250 260 270 280 290 300 NAYSEKELIF PPELQLRKVT SLKLNGFNGI RWYRPLKLKQ VLHLKACYPN AKLIIGNSEV 310 320 330 340 350 360 GVETKFKNAQ YKVLISVTHV PELHTLKVKE DGIHIGSSVR LAQLQNFLRK VILERDSHEI 370 380 390 400 410 420 SSCEAILRQL KWFAGTQIRN VASVGGNICT ASPISDLNPL WMATGATFEI IDVNNNIRTI 430 440 450 460 470 480 PAKDFFLGYR KVDLKPDEIL LSVILPWTRP FEFVKEFKQA HRREDDIALV NAGMRVYIRK 490 500 510 520 530 540 VEGDWIISDV SIIYGGVAAV SHRASKTETF LTGKKWDYGL LDKTFDLLKE DVVLAENAPG 550 560 570 580 590 600 GMVEFRSSLT LSFFFKFFLH VTHEMNIKGF WKDGLHATNL SAIQSFTRPV GVGTQCYELV 610 620 630 640 650 660 RQGTAVGQPV VHTSAMLQVT GEAEYTDDTP TPPNTLHAAL VLSTKAHARI LSIDASLAKS 670 680 690 700 710 720 SPGFAGLFLS KDVPGANHTG PVIHDEEVFA SDVVTCVGQI VGLVVADTRD NAKAAANKVN 730 740 750 760 770 780 IEYSELPAIL SIEEAVKAGS FHPNSKRCLV KGNVEQCFLS GACDRIIEGK VQVGGQEHFY 790 800 810 820 830 840 MEPQSTLVWP VDSGNEIHMI SSTQAPQKHQ KYVANVLGLP QSRVVCKTKR IGGGFGGKET 850 860 870 880 890 900 RSAIFAAAAS VAAYCLRQPV KLVLDRDIDM MTTGQRHSFL GKYKVGFTDD GKILALDLDV 910 920 930 940 950 960 YNNGGHSHDL SLPVLERAMF HSDNVYDIPN VRVNGQVCFT NFPSNTAFRG FGGPQAMLIA 970 980 990 1000 1010 1020 ENWIQHMATE LKRSPEEIKE LNFQSEGSVL HYGQLLQNCT IHSVWDELKV SCNFMEARKA 1030 1040 1050 1060 1070 1080 VIDFNNNNRW RKRGIAMVPT KFGISFTTKF MNQAGALVQV YTDGTVLVTH GGVEMGQGLH 1090 1100 1110 1120 1130 1140 TKVAQVAASS FNIPLSSIFI SETSTDKVPN ATPTAASASS DLYGAAVLDA CQQIMARMEP 1150 1160 1170 1180 1190 1200 VASRGNHKSF AELVLACYLE RIDLSAHGFY ITPDVGFDWV SGKGTPFYYF TYGAAFAEVE 1210 1220 1230 1240 1250 1260 IDTLTGDFHT RTVDIVMDLG CSINPAIDIG QIEGGFIQGL GWAALEELKW GDDNHKWIRP 1270 1280 1290 1300 1310 1320 GHLFTCGPGS YKIPSVNDIP LNFKVSLLKG VLNPKVIHSS KAVGEPPFFL GSAVLFAIKD 1330 1340 1350 1360 AISAARAEEG HFDWFPLDSP ATPERIRMAC VDSITKKFAS VYYRPKLSV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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], GENOME REANNOTATION. Strain: cv. Nipponbare.
[2]	"The map-based sequence of the rice genome." International rice genome sequencing project (IRGSP) Nature 436:793-800(2005) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
RefSeq	NP_001050420.1. NM_001056955.1.
UniGene	Os.10786.
3D structure databases
ProteinModelPortal	Q6AUV1.
ModBase	Search...
Proteomic databases
PRIDE	Q6AUV1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	LOC_Os03g31550.1; LOC_Os03g31550.1; LOC_Os03g31550.
GeneID	4333171.
KEGG	dosa:Os03t0429800-01. osa:4333171.
Organism-specific databases
Gramene	Q6AUV1.
Phylogenomic databases
HOGENOM	HOG000191197.
KO	K00106.
OMA	VASCNED.
ProtClustDB	PLN02906.
Gene expression databases
ArrayExpress	Q6AUV1.
Family and domain databases
Gene3D	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.
InterPro	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]
Pfam	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]
PIRSF	PIRSF000127. Xanthine_DH. 1 hit.
SMART	SM01008. Ald_Xan_dh_C. 1 hit. SM01092. CO_deh_flav_C. 1 hit. [Graphical view]
SUPFAM	SSF47741. 2Fe-2S_bind. 1 hit. SSF56003. Ald_xan_DH_mo_bd. 1 hit. SSF54665. Aldxan_dh_hamm. 1 hit. SSF55447. CO_deh_flav_C. 1 hit. SSF56176. FAD-binding_2. 1 hit. SSF54292. Ferredoxin. 1 hit.
PROSITE	PS00197. 2FE2S_FER_1. 1 hit. PS51085. 2FE2S_FER_2. 1 hit. PS51387. FAD_PCMH. 1 hit. PS00559. MOLYBDOPTERIN_EUK. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

XDH_ORYSJ

Accession

Primary (citable) accession number: Q6AUV1
Secondary accession number(s): Q10J86

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2012
Last sequence update:	September 13, 2004
Last modified:	April 3, 2013
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program