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F4JLI5 (XDH2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 18. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Xanthine dehydrogenase 2
Short name=AtXDH2
EC=1.17.1.4
Gene names
Name:XDH2
Ordered Locus Names:At4g34900
ORF Names:T11I11.140
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length1353 AA.
Sequence statusComplete.
Protein existenceEvidence 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. Regulates the level of ureides and plays a role during plant growth and development and senescence. Ref.4

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.

Tissue specificity

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

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 (Ref.4).

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 CAB45451.1 differs from that shown. Reason: Erroneous gene model prediction.

The sequence CAB80207.1 differs from that shown. Reason: Erroneous gene model prediction.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 13531353Xanthine dehydrogenase 2
PRO_0000417458

Regions

Domain7 – 93872Fe-2S ferredoxin-type
Domain249 – 434186FAD-binding PCMH-type
Nucleotide binding277 – 2848FAD By similarity
Nucleotide binding367 – 3715FAD By similarity

Sites

Active site12891Proton acceptor By similarity
Metal binding451Iron-sulfur (2Fe-2S) 1 By similarity
Metal binding501Iron-sulfur (2Fe-2S) 1 By similarity
Metal binding531Iron-sulfur (2Fe-2S) 1 By similarity
Metal binding751Iron-sulfur (2Fe-2S) 1 By similarity
Metal binding1151Iron-sulfur (2Fe-2S) 2 By similarity
Metal binding1181Iron-sulfur (2Fe-2S) 2 By similarity
Metal binding1511Iron-sulfur (2Fe-2S) 2 By similarity
Metal binding1531Iron-sulfur (2Fe-2S) 2 By similarity
Metal binding7881Molybdenum By similarity
Metal binding8191Molybdenum; via carbonyl oxygen By similarity
Metal binding9331Molybdenum; via amide nitrogen By similarity
Metal binding11001Molybdenum; via amide nitrogen By similarity
Binding site3571FAD By similarity
Binding site3801FAD By similarity
Binding site4241FAD; via amide nitrogen and carbonyl oxygen By similarity
Binding site4421FAD By similarity
Binding site8231Substrate By similarity
Binding site9011Substrate By similarity
Binding site9351Substrate By similarity
Binding site10311Substrate By similarity

Experimental info

Sequence conflict4011V → A in AAR99079. Ref.1

Sequences

Sequence LengthMass (Da)Tools
F4JLI5 [UniParc].

Last modified June 28, 2011. Version 1.
Checksum: FC1AD990E687DD3A

FASTA1,353148,762
        10         20         30         40         50         60 
MEQNEFMEAI MYVNGVRRVL PDGLAHMTLL EYLRDLGLTG TKLGCGEGGC GSCTVMVSSY 

        70         80         90        100        110        120 
DRESKTCVHY AVNACLAPLY SVEGMHVISI EGVGHRKLGL HPLQESLASS HGSQCGFCTP 

       130        140        150        160        170        180 
GFVMSMYALL RSSKNSPSEE EIEECLAGNL CRCTGYRPII DAFRVFAKSD DALYSGLSSL 

       190        200        210        220        230        240 
SLQDGSNICP STGKPCSCGS KTTSEAATCN EDRFQSISYS DIDGAKYTDK ELIFPPELLL 

       250        260        270        280        290        300 
RKLAPLKLGG NEGITWYRPV SLQNLLELKA NFPDAKLLVG NTEVGIEMRL KRLQYPVLIS 

       310        320        330        340        350        360 
AAQVPELNAL NVNDNGIEVG SALRLSELLR LFRKVVKERP AHETSACKAF IEQLKWFAGT 

       370        380        390        400        410        420 
QIRNVACIGG NICTASPISD LNPLWMASRA EFRIINCNGD VRSIPAKDFF LGYRKVDMGS 

       430        440        450        460        470        480 
NEILLSVFLP WTRPLEYVKE FKQAHRRDDD IAIVNGGMRV FLEEKGQQLF VSDASIVYGG 

       490        500        510        520        530        540 
VAPLSLRARN TEELLIGKNW NKCLLQDALK VIQSDVLIKE GAPGGMVEFR KSLTLSFFFK 

       550        560        570        580        590        600 
FFLWVTHHVN NVNPTIETFP PSHMSAVQLV PRFSRIGKQD YETVKQGTSV GLPEVHLSAR 

       610        620        630        640        650        660 
MQVTGEAEYT DDTPLPPCTL HAALVLSKVP HARILSVDDS AAKSSSGFVG LFLAKDVPGN 

       670        680        690        700        710        720 
NMIGPIVADE ELFATDVVTC VGQVIGVLVA DTHENAKTAA RKVDVRYQEL PAILSIKEAI 

       730        740        750        760        770        780 
NAKSFHPNTE RRLRKGDVEL CFQSGQCDRI IEGEVQMGGQ EHFYLEPNGS LVWTIDGGNE 

       790        800        810        820        830        840 
VHMISSTQAP QQHQKYVSHV LGLPMSKVVC KTKRLGGGFG GKETRSAFIA AAASVPSYLL 

       850        860        870        880        890        900 
NRPVKLILDR DVDMMITGHR HSFVGKYKVG FTNEGKILAL DLEIYNNGGN SMDLSLSNLE 

       910        920        930        940        950        960 
RAMFHSDNVY EIPHVRIVGN VCFTNFPSNT AFRGFGGPQG MLITENWIQR IAAELDKIPE 

       970        980        990       1000       1010       1020 
EIKEMNFQVE GSITHYFQSL QHCTLHQLWK ELKVSSNFLK TRREADEFNS HNRWKKRGVA 

      1030       1040       1050       1060       1070       1080 
MVPTKFGISF TTKFMNQAGA LVHVYTDGTV LVTHGGVEMG QGLHTKVAQV AATAFNILLS 

      1090       1100       1110       1120       1130       1140 
SVFVSETSTD KVPNASPTAA SASSDMYGAA VLDACEQIIA RMEPVASKHN FNTFSELASA 

      1150       1160       1170       1180       1190       1200 
CYFQRIDLSA HGFHIVPELE FDWVSGKGNA YRYYTYGAAF AEVEIDTLTG DFHTRKADIM 

      1210       1220       1230       1240       1250       1260 
LDLGYSLNPT IDIGQIEGAF VQGLGWVALE ELKWGDAAHK WIKPGSLLTC GPGSYKIPSI 

      1270       1280       1290       1300       1310       1320 
NDMPFQLNVS LLKGNPNAKA IHSSKAVGEP PFFLAASAFF AIKEAIKAAR SEVGLTNWFP 

      1330       1340       1350 
LETPATPERI RMACFDEFSA PFANSDFCPK LSV

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		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.
IPIIPI00526414.
PIRT10236.
RefSeqNP_195216.2. NM_119656.2.
UniGeneAt.31462.

3D structure databases

ProteinModelPortalF4JLI5.
SMRF4JLI5. Positions 8-168, 230-545, 589-1339.
ModBaseSearch...

Protein-protein interaction databases

STRING3702.AT4G34900.1-P.

Proteomic databases

PRIDEF4JLI5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT4G34900.1; AT4G34900.1; AT4G34900.
GeneID829642.
KEGGath:AT4G34900.

Organism-specific databases

TAIRAt4g34900.

Phylogenomic databases

HOGENOMHOG000191197.
KOK00106.
OMAERIHISE.

Family and domain databases

Gene3D1.10.150.120. 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.
InterProIPR002888. 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]
PfamPF01315. 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]
PIRSFPIRSF000127. Xanthine_DH. 1 hit.
SMARTSM01008. Ald_Xan_dh_C. 1 hit.
SM01092. CO_deh_flav_C. 1 hit.
[Graphical view]
SUPFAMSSF47741. 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.
PROSITEPS00197. 2FE2S_FER_1. 1 hit.
PS51085. 2FE2S_FER_2. 1 hit.
PS51387. FAD_PCMH. 1 hit.
PS00559. MOLYBDOPTERIN_EUK. False negative.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameXDH2_ARATH
AccessionPrimary (citable) accession number: F4JLI5
Secondary accession number(s): Q6R2R5, Q9SW45
Entry history
Integrated into UniProtKB/Swiss-Prot: May 16, 2012
Last sequence update: June 28, 2011
Last modified: May 1, 2013
This is version 18 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

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