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Protein

Xanthine dehydrogenase

Gene

xdh

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid (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 bindingi56 – 561Iron-sulfur 1By similarity
Metal bindingi61 – 611Iron-sulfur 1By similarity
Metal bindingi64 – 641Iron-sulfur 1By similarity
Metal bindingi89 – 891Iron-sulfur 1By similarity
Metal bindingi129 – 1291Iron-sulfur 2By similarity
Metal bindingi132 – 1321Iron-sulfur 2By similarity
Metal bindingi164 – 1641Iron-sulfur 2By similarity
Metal bindingi166 – 1661Iron-sulfur 2By similarity
Binding sitei366 – 3661FADBy similarity
Binding sitei389 – 3891FADBy similarity
Binding sitei437 – 4371FAD; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei455 – 4551FADBy similarity
Metal bindingi805 – 8051MolybdenumBy similarity
Metal bindingi836 – 8361Molybdenum; via carbonyl oxygenBy similarity
Binding sitei840 – 8401SubstrateBy similarity
Binding sitei918 – 9181SubstrateBy similarity
Metal bindingi950 – 9501Molybdenum; via amide nitrogenBy similarity
Binding sitei952 – 9521SubstrateBy similarity
Binding sitei1048 – 10481Substrate; via amide nitrogenBy similarity
Metal bindingi1117 – 11171Molybdenum; via amide nitrogenBy similarity
Active sitei1302 – 13021Proton acceptorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi281 – 2888FADBy similarity
Nucleotide bindingi376 – 3805FADBy similarity

GO - Molecular functioni

GO - Biological processi

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_302287. Purine catabolism.
REACT_332276. Vitamins B6 activation to pyridoxal phosphate.

Names & Taxonomyi

Protein namesi
Recommended name:
Xanthine dehydrogenase (EC:1.17.1.4)
Short name:
XD
Gene namesi
Name:xdh
ORF Names:DDB_G0291047
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195 Componentsi: Chromosome 5, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0291047. xdh.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Peroxisome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 13581358Xanthine dehydrogenasePRO_0000327650Add
BLAST

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi44689.DDB0230176.

Structurei

3D structure databases

ProteinModelPortaliQ54FB7.
SMRiQ54FB7. Positions 18-181.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini18 – 107902Fe-2S ferredoxin-typePROSITE-ProRule annotationAdd
BLAST
Domaini253 – 447195FAD-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

eggNOGiCOG4630.
InParanoidiQ54FB7.
KOiK00106.
OMAiFHMENSY.
PhylomeDBiQ54FB7.

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.

Q54FB7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIDDENLNGK EPFLKKENQL LFFLNGEKVL INEPNPELST LDYIRSIGLT
60 70 80 90 100
GLKRGCSEGA CGSCTFMLSN VVKDDNDTFR IVHRAVNGCL YPLCALDGMA
110 120 130 140 150
VTTIEGLGNI DKGLHSIQER ISENSGSQCG FCTPGIIMAL YAFLRSNPNS
160 170 180 190 200
TQKDIEQNFD GNLCRCTGYR PILDAAKSFA NQPSDEQLVE LPLPPMATID
210 220 230 240 250
DKKDDTQMIC PGTGKPCNCK TKTSHIPNKP MELNSEPIFP PFLMEYKKES
260 270 280 290 300
LKFTGSRVTW YTPTTLEELL KIKKEKTNAK IVVGNTEIGI ETRFRSIVYP
310 320 330 340 350
TIICPTRVEE LIQIQKEDNG VRVGASVTLT EMKSYLNGII KSSENDEIAN
360 370 380 390 400
KKNGTFKAII SQLKWFAGNQ VRNAASIGGN LCTASPISDL NPVLLAAGAV
410 420 430 440 450
LTMVSLDDNG AKVRRQVPIN QFFLRYRVVD IKPEEILESV FIPYTRPLEF
460 470 480 490 500
IQAYKQSRRR EDDIAIVSCC FRVLLEPIAE SASNTVDSNF KIKDCVLAYG
510 520 530 540 550
GMNVKAVTCE KTEKQLIGSV WSRELLNDAC LNLESDLPLA AGAPGGMIEY
560 570 580 590 600
RRSLTTGFFF KYFLTVSKQL YQISNGNPLY LVSDKEKSAT DAYSRPLSFG
610 620 630 640 650
EQNYQTQPDK HPITQPIKHQ SADKQVTGEA LYVDDVKMKS LYAVMVPSLK
660 670 680 690 700
AHANIKSVDA SKALKAPGVK AFFSAKDIPG INDCGPVIHD EEVFVTKTAL
710 720 730 740 750
FHGAPIGCIV AETHIQALEA SKLVAIEYEE LPAITSIEDA ISKQSFFPFT
760 770 780 790 800
HLLKDGDMEK GWSESDHIID GEFKVGAQEH FYLEPNGTLV IPGEGKELTV
810 820 830 840 850
ISSTQNPTKT QAIVASVLGI GQNQVVCKLK RLGGGFGGKE TRSIFSSCVA
860 870 880 890 900
AIASYHMKEP VRIILDRDTD MSTTGTRHPF IARYRVGFTK EGLIKALDLE
910 920 930 940 950
LYADAGFSYD ISVGVLDRAI FHSENSYKIP NVNILGRLCK TNLPSNTAFR
960 970 980 990 1000
GYGGPQAMII CENWVEKISK TLGMDSYKIR ELNFYKEAEV TAYRQSVVNN
1010 1020 1030 1040 1050
MMKRVWDELM VKSNYHQRLI AVEKFNKENR YKKRGISIIP TKFGMSFTVK
1060 1070 1080 1090 1100
TLNQAGALVH VYTDGTILVT HGGTEMGQGL NTKMIQIAAR AFNVPVSDVF
1110 1120 1130 1140 1150
ISETSTDKVP NTAPTAASVS SDLNGMAVLD ACQQILLRME PIREKNPNVP
1160 1170 1180 1190 1200
FKQLCTLCFV ERVNLSANGF YATPNVGYMF KDSGVGEGTP FNYFNFGAAC
1210 1220 1230 1240 1250
SEVEIDTLTG DHTTLRSDVI LDVGDSLNPT IDIGQVEGAF VQGMGWSTLE
1260 1270 1280 1290 1300
EVVTFPSGYM FTRGPSTYKI PGFNDVPIEF NVSLLGDAPN PKAIHSSKGV
1310 1320 1330 1340 1350
GEPPLFLGSS VYFAIRQAIT AARLENNLTN WFDLQSPATC ERIRTSCLDN

FVLQFRKQ
Length:1,358
Mass (Da):149,928
Last modified:May 24, 2005 - v1
Checksum:iAF9AEE1059FE076F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000174 Genomic DNA. Translation: EAL61954.1.
RefSeqiXP_635420.1. XM_630328.1.

Genome annotation databases

EnsemblProtistsiDDB0230176; DDB0230176; DDB_G0291047.
GeneIDi8627921.
KEGGiddi:DDB_G0291047.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000174 Genomic DNA. Translation: EAL61954.1.
RefSeqiXP_635420.1. XM_630328.1.

3D structure databases

ProteinModelPortaliQ54FB7.
SMRiQ54FB7. Positions 18-181.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0230176.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0230176; DDB0230176; DDB_G0291047.
GeneIDi8627921.
KEGGiddi:DDB_G0291047.

Organism-specific databases

dictyBaseiDDB_G0291047. xdh.

Phylogenomic databases

eggNOGiCOG4630.
InParanoidiQ54FB7.
KOiK00106.
OMAiFHMENSY.
PhylomeDBiQ54FB7.

Enzyme and pathway databases

ReactomeiREACT_302287. Purine catabolism.
REACT_332276. Vitamins B6 activation to pyridoxal phosphate.

Miscellaneous databases

PROiQ54FB7.

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...

Publicationsi

  1. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.

Entry informationi

Entry nameiXDH_DICDI
AccessioniPrimary (citable) accession number: Q54FB7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: May 24, 2005
Last modified: June 24, 2015
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.