Xanthine dehydrogenase - Dictyostelium discoideum (Slime mold)

Preferred order of sections

Names and origin

Protein names

Recommended name:
Xanthine dehydrogenase
Short name=XD
EC=1.17.1.4

Gene names

Name:	xdh
ORF Names:	DDB_G0291047

Organism

Dictyostelium discoideum (Slime mold) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	1358 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid 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.
Subcellular location	Peroxisome By similarity.
Sequence similarities	Belongs to the xanthine dehydrogenase family. Contains 1 2Fe-2S ferredoxin-type domain. Contains 1 FAD-binding PCMH-type domain.

Ontologies

Keywords
Cellular component	Peroxisome
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	xanthine catabolic process Inferred from sequence or structural similarity. Source: UniProtKB
Cellular_component	peroxisome Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	2 iron, 2 sulfur cluster binding Inferred from sequence or structural similarity. Source: UniProtKB 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 sequence or structural similarity. Source: UniProtKB iron ion binding Inferred from electronic annotation. Source: InterPro molybdopterin cofactor binding Inferred from sequence or structural similarity. Source: UniProtKB xanthine dehydrogenase activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1358

1358

Xanthine dehydrogenase

PRO_0000327650

Regions

Domain

18 – 107

90

2Fe-2S ferredoxin-type

Domain

253 – 447

195

FAD-binding PCMH-type

Nucleotide binding

281 – 288

8

FAD By similarity

Nucleotide binding

376 – 380

5

FAD By similarity

Sites

Active site

1302

1

Proton acceptor By similarity

Metal binding

56

1

Iron-sulfur 1 By similarity

Metal binding

61

1

Iron-sulfur 1 By similarity

Metal binding

64

1

Iron-sulfur 1 By similarity

Metal binding

89

1

Iron-sulfur 1 By similarity

Metal binding

129

1

Iron-sulfur 2 By similarity

Metal binding

132

1

Iron-sulfur 2 By similarity

Metal binding

164

1

Iron-sulfur 2 By similarity

Metal binding

166

1

Iron-sulfur 2 By similarity

Metal binding

805

1

Molybdenum By similarity

Metal binding

836

1

Molybdenum; via carbonyl oxygen By similarity

Metal binding

950

1

Molybdenum; via amide nitrogen By similarity

Metal binding

1117

1

Molybdenum; via amide nitrogen By similarity

Binding site

366

1

FAD By similarity

Binding site

389

1

FAD By similarity

Binding site

437

1

FAD; via amide nitrogen and carbonyl oxygen By similarity

Binding site

455

1

FAD By similarity

Binding site

840

1

Substrate By similarity

Binding site

918

1

Substrate By similarity

Binding site

952

1

Substrate By similarity

Binding site

1048

1

Substrate; via amide nitrogen By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q54FB7 [UniParc].

Last modified May 24, 2005. Version 1.
Checksum: AF9AEE1059FE076F
Show »

FASTA

1,358

149,928

        10         20         30         40         50         60 
MIDDENLNGK EPFLKKENQL LFFLNGEKVL INEPNPELST LDYIRSIGLT GLKRGCSEGA 

        70         80         90        100        110        120 
CGSCTFMLSN VVKDDNDTFR IVHRAVNGCL YPLCALDGMA VTTIEGLGNI DKGLHSIQER 

       130        140        150        160        170        180 
ISENSGSQCG FCTPGIIMAL YAFLRSNPNS TQKDIEQNFD GNLCRCTGYR PILDAAKSFA 

       190        200        210        220        230        240 
NQPSDEQLVE LPLPPMATID DKKDDTQMIC PGTGKPCNCK TKTSHIPNKP MELNSEPIFP 

       250        260        270        280        290        300 
PFLMEYKKES LKFTGSRVTW YTPTTLEELL KIKKEKTNAK IVVGNTEIGI ETRFRSIVYP 

       310        320        330        340        350        360 
TIICPTRVEE LIQIQKEDNG VRVGASVTLT EMKSYLNGII KSSENDEIAN KKNGTFKAII 

       370        380        390        400        410        420 
SQLKWFAGNQ VRNAASIGGN LCTASPISDL NPVLLAAGAV LTMVSLDDNG AKVRRQVPIN 

       430        440        450        460        470        480 
QFFLRYRVVD IKPEEILESV FIPYTRPLEF IQAYKQSRRR EDDIAIVSCC FRVLLEPIAE 

       490        500        510        520        530        540 
SASNTVDSNF KIKDCVLAYG GMNVKAVTCE KTEKQLIGSV WSRELLNDAC LNLESDLPLA 

       550        560        570        580        590        600 
AGAPGGMIEY RRSLTTGFFF KYFLTVSKQL YQISNGNPLY LVSDKEKSAT DAYSRPLSFG 

       610        620        630        640        650        660 
EQNYQTQPDK HPITQPIKHQ SADKQVTGEA LYVDDVKMKS LYAVMVPSLK AHANIKSVDA 

       670        680        690        700        710        720 
SKALKAPGVK AFFSAKDIPG INDCGPVIHD EEVFVTKTAL FHGAPIGCIV AETHIQALEA 

       730        740        750        760        770        780 
SKLVAIEYEE LPAITSIEDA ISKQSFFPFT HLLKDGDMEK GWSESDHIID GEFKVGAQEH 

       790        800        810        820        830        840 
FYLEPNGTLV IPGEGKELTV ISSTQNPTKT QAIVASVLGI GQNQVVCKLK RLGGGFGGKE 

       850        860        870        880        890        900 
TRSIFSSCVA AIASYHMKEP VRIILDRDTD MSTTGTRHPF IARYRVGFTK EGLIKALDLE 

       910        920        930        940        950        960 
LYADAGFSYD ISVGVLDRAI FHSENSYKIP NVNILGRLCK TNLPSNTAFR GYGGPQAMII 

       970        980        990       1000       1010       1020 
CENWVEKISK TLGMDSYKIR ELNFYKEAEV TAYRQSVVNN MMKRVWDELM VKSNYHQRLI 

      1030       1040       1050       1060       1070       1080 
AVEKFNKENR YKKRGISIIP TKFGMSFTVK TLNQAGALVH VYTDGTILVT HGGTEMGQGL 

      1090       1100       1110       1120       1130       1140 
NTKMIQIAAR AFNVPVSDVF ISETSTDKVP NTAPTAASVS SDLNGMAVLD ACQQILLRME 

      1150       1160       1170       1180       1190       1200 
PIREKNPNVP FKQLCTLCFV ERVNLSANGF YATPNVGYMF KDSGVGEGTP FNYFNFGAAC 

      1210       1220       1230       1240       1250       1260 
SEVEIDTLTG DHTTLRSDVI LDVGDSLNPT IDIGQVEGAF VQGMGWSTLE EVVTFPSGYM 

      1270       1280       1290       1300       1310       1320 
FTRGPSTYKI PGFNDVPIEF NVSLLGDAPN PKAIHSSKGV GEPPLFLGSS VYFAIRQAIT 

      1330       1340       1350 
AARLENNLTN WFDLQSPATC ERIRTSCLDN FVLQFRKQ

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References

[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.

Kuspa A.
Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: AX4.

+

Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AAFI02000174 Genomic DNA. Translation: EAL61954.1.
RefSeq	XP_635420.1. XM_630328.1.
3D structure databases
HSSP	HSSP built from PDB template 1FIQ based on UniProtKB P80457.
ProteinModelPortal	Q54FB7.
SMR	Q54FB7. Positions 18-181.
ModBase	Search...
Protein-protein interaction databases
STRING	44689.DDB_0230176.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0230176; DDB0230176; DDB_G0291047.
GeneID	8627921.
KEGG	ddi:DDB_G0291047.
Organism-specific databases
dictyBase	DDB_G0291047. xdh.
Phylogenomic databases
eggNOG	COG4630.
KO	K00106.
OMA	FKNMLFP.
ProtClustDB	CLSZ2429618.
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_DICDI

Accession

Primary (citable) accession number: Q54FB7

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 8, 2008
Last sequence update:	May 24, 2005
Last modified:	May 1, 2013
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Relevant documents

Dictyostelium discoideum

Dictyostelium discoideum: entries, gene names and cross-references to dictyBase

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents