XDH_DICDI
ID XDH_DICDI Reviewed; 1358 AA.
AC Q54FB7;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Xanthine dehydrogenase;
DE Short=XD;
DE EC=1.17.1.4;
GN Name=xdh; ORFNames=DDB_G0291047;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
CC -!- FUNCTION: Key enzyme in purine degradation. Catalyzes the oxidation of
CC hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric
CC acid (By similarity). {ECO:0000250}.
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 -!- 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 -!- 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 -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000250|UniProtKB:P22985};
CC Note=Binds 2 [2Fe-2S] clusters per subunit.
CC {ECO:0000250|UniProtKB:P22985};
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the xanthine dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; AAFI02000174; EAL61954.1; -; Genomic_DNA.
DR RefSeq; XP_635420.1; XM_630328.1.
DR AlphaFoldDB; Q54FB7; -.
DR SMR; Q54FB7; -.
DR STRING; 44689.DDB0230176; -.
DR PaxDb; Q54FB7; -.
DR EnsemblProtists; EAL61954; EAL61954; DDB_G0291047.
DR GeneID; 8627921; -.
DR KEGG; ddi:DDB_G0291047; -.
DR dictyBase; DDB_G0291047; xdh.
DR eggNOG; KOG0430; Eukaryota.
DR HOGENOM; CLU_001681_1_2_1; -.
DR InParanoid; Q54FB7; -.
DR OMA; DIGYVWG; -.
DR PhylomeDB; Q54FB7; -.
DR Reactome; R-DDI-74259; Purine catabolism.
DR Reactome; R-DDI-964975; Vitamins B6 activation to pyridoxal phosphate.
DR Reactome; R-DDI-9748787; Azathioprine ADME.
DR PRO; PR:Q54FB7; -.
DR Proteomes; UP000002195; Chromosome 5.
DR GO; GO:0005777; C:peroxisome; IEA:UniProtKB-SubCell.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; ISS:UniProtKB.
DR GO; GO:0071949; F:FAD binding; IEA:InterPro.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; ISS:UniProtKB.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0043546; F:molybdopterin cofactor binding; ISS:UniProtKB.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0004854; F:xanthine dehydrogenase activity; ISS:UniProtKB.
DR GO; GO:0009115; P:xanthine catabolic process; ISS:UniProtKB.
DR CDD; cd00207; fer2; 1.
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 3: Inferred from homology;
KW 2Fe-2S; FAD; Flavoprotein; Iron; Iron-sulfur; Metal-binding; Molybdenum;
KW NAD; Oxidoreductase; Peroxisome; Reference proteome.
FT CHAIN 1..1358
FT /note="Xanthine dehydrogenase"
FT /id="PRO_0000327650"
FT DOMAIN 18..107
FT /note="2Fe-2S ferredoxin-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT DOMAIN 253..447
FT /note="FAD-binding PCMH-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00718"
FT ACT_SITE 1302
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 56
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P22985"
FT BINDING 61
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P22985"
FT BINDING 64
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P22985"
FT BINDING 89
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P22985"
FT BINDING 129
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P22985"
FT BINDING 132
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P22985"
FT BINDING 164
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P22985"
FT BINDING 166
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P22985"
FT BINDING 281..288
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 366
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 376..380
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 389
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 437
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 455
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 805
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 836
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 840
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 918
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 950
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 952
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 1048
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 1117
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"
SQ SEQUENCE 1358 AA; 149928 MW; AF9AEE1059FE076F CRC64;
MIDDENLNGK EPFLKKENQL LFFLNGEKVL INEPNPELST LDYIRSIGLT GLKRGCSEGA
CGSCTFMLSN VVKDDNDTFR IVHRAVNGCL YPLCALDGMA VTTIEGLGNI DKGLHSIQER
ISENSGSQCG FCTPGIIMAL YAFLRSNPNS TQKDIEQNFD GNLCRCTGYR PILDAAKSFA
NQPSDEQLVE LPLPPMATID DKKDDTQMIC PGTGKPCNCK TKTSHIPNKP MELNSEPIFP
PFLMEYKKES LKFTGSRVTW YTPTTLEELL KIKKEKTNAK IVVGNTEIGI ETRFRSIVYP
TIICPTRVEE LIQIQKEDNG VRVGASVTLT EMKSYLNGII KSSENDEIAN KKNGTFKAII
SQLKWFAGNQ VRNAASIGGN LCTASPISDL NPVLLAAGAV LTMVSLDDNG AKVRRQVPIN
QFFLRYRVVD IKPEEILESV FIPYTRPLEF IQAYKQSRRR EDDIAIVSCC FRVLLEPIAE
SASNTVDSNF KIKDCVLAYG GMNVKAVTCE KTEKQLIGSV WSRELLNDAC LNLESDLPLA
AGAPGGMIEY RRSLTTGFFF KYFLTVSKQL YQISNGNPLY LVSDKEKSAT DAYSRPLSFG
EQNYQTQPDK HPITQPIKHQ SADKQVTGEA LYVDDVKMKS LYAVMVPSLK AHANIKSVDA
SKALKAPGVK AFFSAKDIPG INDCGPVIHD EEVFVTKTAL FHGAPIGCIV AETHIQALEA
SKLVAIEYEE LPAITSIEDA ISKQSFFPFT HLLKDGDMEK GWSESDHIID GEFKVGAQEH
FYLEPNGTLV IPGEGKELTV ISSTQNPTKT QAIVASVLGI GQNQVVCKLK RLGGGFGGKE
TRSIFSSCVA AIASYHMKEP VRIILDRDTD MSTTGTRHPF IARYRVGFTK EGLIKALDLE
LYADAGFSYD ISVGVLDRAI FHSENSYKIP NVNILGRLCK TNLPSNTAFR GYGGPQAMII
CENWVEKISK TLGMDSYKIR ELNFYKEAEV TAYRQSVVNN MMKRVWDELM VKSNYHQRLI
AVEKFNKENR YKKRGISIIP TKFGMSFTVK TLNQAGALVH VYTDGTILVT HGGTEMGQGL
NTKMIQIAAR AFNVPVSDVF ISETSTDKVP NTAPTAASVS SDLNGMAVLD ACQQILLRME
PIREKNPNVP FKQLCTLCFV ERVNLSANGF YATPNVGYMF KDSGVGEGTP FNYFNFGAAC
SEVEIDTLTG DHTTLRSDVI LDVGDSLNPT IDIGQVEGAF VQGMGWSTLE EVVTFPSGYM
FTRGPSTYKI PGFNDVPIEF NVSLLGDAPN PKAIHSSKGV GEPPLFLGSS VYFAIRQAIT
AARLENNLTN WFDLQSPATC ERIRTSCLDN FVLQFRKQ
