SPS3_DANRE
ID SPS3_DANRE Reviewed; 447 AA.
AC Q66I14; Q802F1;
DT 22-APR-2020, integrated into UniProtKB/Swiss-Prot.
DT 22-APR-2020, sequence version 2.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Selenide, water dikinase 3 {ECO:0000305};
DE EC=2.7.9.3 {ECO:0000250|UniProtKB:P49903};
DE AltName: Full=Selenophosphate synthetase 3 {ECO:0000305};
GN Name=sephs3 {ECO:0000312|ZFIN:ZDB-GENE-030327-5};
GN Synonyms=sephs2 {ECO:0000312|ZFIN:ZDB-GENE-030327-5},
GN sps2 {ECO:0000312|ZFIN:ZDB-GENE-030327-5};
GN ORFNames=zgc:92096 {ECO:0000312|EMBL:AAH81590.1};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000312|EMBL:AAH81590.1};
RN [1] {ECO:0000312|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000312|Proteomes:UP000000437};
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2] {ECO:0000312|EMBL:AAH81590.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000312|EMBL:AAO65274.1}
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-371, AND TISSUE SPECIFICITY.
RC TISSUE=Embryo {ECO:0000312|EMBL:AAO65274.1};
RX PubMed=12915322; DOI=10.1016/s1567-133x(03)00054-1;
RA Thisse C., Degrave A., Kryukov G.V., Gladyshev V.N., Obrecht-Pflumio S.,
RA Krol A., Thisse B., Lescure A.;
RT "Spatial and temporal expression patterns of selenoprotein genes during
RT embryogenesis in zebrafish.";
RL Gene Expr. Patterns 3:525-532(2003).
CC -!- FUNCTION: Synthesizes selenophosphate from selenide and ATP.
CC {ECO:0000250|UniProtKB:P49903}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O + hydrogenselenide = AMP + 2 H(+) + phosphate +
CC selenophosphate; Xref=Rhea:RHEA:18737, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16144, ChEBI:CHEBI:29317,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456215; EC=2.7.9.3;
CC Evidence={ECO:0000250|UniProtKB:P49903};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P49903};
CC Note=Binds 1 Mg(2+) ion per monomer. {ECO:0000250|UniProtKB:P49903};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P49903}.
CC -!- TISSUE SPECIFICITY: In the embryo, expressed in retina, olfactory
CC vesicles, tectum, pronephros ducts and myotomes at 24 hours post-
CC fertilization and in retina, tectum, liver and intestinal bulb 3 days
CC after fertilization. {ECO:0000269|PubMed:12915322}.
CC -!- SIMILARITY: Belongs to the selenophosphate synthase 1 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH81590.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
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DR EMBL; CR354375; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC081590; AAH81590.1; ALT_SEQ; mRNA.
DR EMBL; AY221265; AAO65274.1; -; mRNA.
DR RefSeq; NP_001004295.2; NM_001004295.2.
DR STRING; 7955.ENSDARP00000026731; -.
DR PaxDb; Q66I14; -.
DR PRIDE; Q66I14; -.
DR DNASU; 352933; -.
DR GeneID; 352933; -.
DR KEGG; dre:352933; -.
DR CTD; 352933; -.
DR ZFIN; ZDB-GENE-030327-5; sephs3.
DR eggNOG; KOG3939; Eukaryota.
DR HOGENOM; CLU_032859_1_0_1; -.
DR InParanoid; Q66I14; -.
DR OrthoDB; 1166567at2759; -.
DR PhylomeDB; Q66I14; -.
DR TreeFam; TF313811; -.
DR Reactome; R-DRE-2408557; Selenocysteine synthesis.
DR PRO; PR:Q66I14; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR ExpressionAtlas; Q66I14; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004756; F:selenide, water dikinase activity; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0016260; P:selenocysteine biosynthetic process; IBA:GO_Central.
DR CDD; cd02195; SelD; 1.
DR Gene3D; 3.30.1330.10; -; 1.
DR Gene3D; 3.90.650.10; -; 1.
DR InterPro; IPR010918; PurM-like_C_dom.
DR InterPro; IPR036676; PurM-like_C_sf.
DR InterPro; IPR016188; PurM-like_N.
DR InterPro; IPR036921; PurM-like_N_sf.
DR InterPro; IPR004536; SPS/SelD.
DR PANTHER; PTHR10256; PTHR10256; 1.
DR Pfam; PF00586; AIRS; 1.
DR Pfam; PF02769; AIRS_C; 1.
DR SUPFAM; SSF55326; SSF55326; 1.
DR SUPFAM; SSF56042; SSF56042; 1.
DR TIGRFAMs; TIGR00476; selD; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Kinase; Magnesium; Metal-binding; Nucleotide-binding;
KW Reference proteome; Selenium; Selenocysteine; Transferase.
FT CHAIN 1..447
FT /note="Selenide, water dikinase 3"
FT /id="PRO_0000449527"
FT ACT_SITE 50
FT /evidence="ECO:0000255"
FT BINDING 53
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 103..105
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 105
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 123
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 146
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 146
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 197..200
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 301
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT SITE 53
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250|UniProtKB:P16456"
FT NON_STD 50
FT /note="Selenocysteine"
FT /evidence="ECO:0000312|EMBL:AAO65274.1"
SQ SEQUENCE 447 AA; 47456 MW; 2ACBD3DC280107C9 CRC64;
MSGSEPPSGD SGGAGGYAVF YPAGYQALNP EEHGLDRGFR LTAFSDMKGU GCKVPQETLL
KLLQGLEPDR PPGEDGGLGT GVGDETADFG LVSAAQGPRL GIGMDSCVIP LRHGGLSLVQ
TTDFFYPLVE DPYMMGRIAC ANVLSDLYAM GITECDNMLM LLSVSQKMNE KERDLVLPLM
MKGFRDAAEE GGTSVTGGQT VINPWIIIGG VASVVCQPND FILPDGAVPG DVLVLTKPLG
TQVAVNAHQW LDIPEKWNKI KLVISREEVE QAYQEAMLNM ATLNRTAAAL MHKFNAHAAT
DITGFGIIGH ARNLAKQQKN DVAFVIHNLP IISKMAAISK AGGNLFGLLQ GTSSETSGGL
LICLPREQAA RFCAEMKSSR MGLLGAGQDG GVGDGQQAWI IGIVEKGNRC ARIIDKPRII
EVPYRGSVVS VQEGSNNNAS PPEVQLA
