SPS2_LEIMA
ID SPS2_LEIMA Reviewed; 398 AA.
AC Q4Q0M0; Q8MXD3;
DT 02-DEC-2020, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2005, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Selenide, water dikinase {ECO:0000305};
DE EC=2.7.9.3 {ECO:0000269|PubMed:18812192};
DE AltName: Full=LmselD {ECO:0000303|PubMed:18812192};
DE AltName: Full=Selenophosphate synthetase 2 {ECO:0000305};
GN Name=SPS2 {ECO:0000305}; Synonyms=SelD {ECO:0000303|PubMed:18812192};
GN ORFNames=LMJF_36_5410 {ECO:0000312|EMBL:CAJ09514.1};
OS Leishmania major.
OC Eukaryota; Discoba; Euglenozoa; Kinetoplastea; Metakinetoplastina;
OC Trypanosomatida; Trypanosomatidae; Leishmaniinae; Leishmania.
OX NCBI_TaxID=5664 {ECO:0000312|Proteomes:UP000000542};
RN [1] {ECO:0000312|EMBL:AAG35734.3}
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RX PubMed=15354357; DOI=10.1080/10425170310001623653;
RA Jayakumar P.C., Musande V.V., Shouche Y.S., Patole M.S.;
RT "The Selenophosphate synthetase gene from Leishmania major.";
RL DNA Seq. 15:66-70(2004).
RN [2] {ECO:0000312|Proteomes:UP000000542}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MHOM/IL/81/Friedlin {ECO:0000312|Proteomes:UP000000542};
RX PubMed=16020728; DOI=10.1126/science.1112680;
RA Ivens A.C., Peacock C.S., Worthey E.A., Murphy L., Aggarwal G.,
RA Berriman M., Sisk E., Rajandream M.A., Adlem E., Aert R., Anupama A.,
RA Apostolou Z., Attipoe P., Bason N., Bauser C., Beck A., Beverley S.M.,
RA Bianchettin G., Borzym K., Bothe G., Bruschi C.V., Collins M., Cadag E.,
RA Ciarloni L., Clayton C., Coulson R.M.R., Cronin A., Cruz A.K., Davies R.M.,
RA De Gaudenzi J., Dobson D.E., Duesterhoeft A., Fazelina G., Fosker N.,
RA Frasch A.C., Fraser A., Fuchs M., Gabel C., Goble A., Goffeau A.,
RA Harris D., Hertz-Fowler C., Hilbert H., Horn D., Huang Y., Klages S.,
RA Knights A., Kube M., Larke N., Litvin L., Lord A., Louie T., Marra M.,
RA Masuy D., Matthews K., Michaeli S., Mottram J.C., Mueller-Auer S.,
RA Munden H., Nelson S., Norbertczak H., Oliver K., O'neil S., Pentony M.,
RA Pohl T.M., Price C., Purnelle B., Quail M.A., Rabbinowitsch E.,
RA Reinhardt R., Rieger M., Rinta J., Robben J., Robertson L., Ruiz J.C.,
RA Rutter S., Saunders D., Schaefer M., Schein J., Schwartz D.C., Seeger K.,
RA Seyler A., Sharp S., Shin H., Sivam D., Squares R., Squares S., Tosato V.,
RA Vogt C., Volckaert G., Wambutt R., Warren T., Wedler H., Woodward J.,
RA Zhou S., Zimmermann W., Smith D.F., Blackwell J.M., Stuart K.D.,
RA Barrell B.G., Myler P.J.;
RT "The genome of the kinetoplastid parasite, Leishmania major.";
RL Science 309:436-442(2005).
RN [3] {ECO:0000312|Proteomes:UP000000542}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MHOM/IL/81/Friedlin {ECO:0000312|Proteomes:UP000000542};
RX PubMed=22038252; DOI=10.1101/gr.122945.111;
RA Rogers M.B., Hilley J.D., Dickens N.J., Wilkes J., Bates P.A.,
RA Depledge D.P., Harris D., Her Y., Herzyk P., Imamura H., Otto T.D.,
RA Sanders M., Seeger K., Dujardin J.C., Berriman M., Smith D.F.,
RA Hertz-Fowler C., Mottram J.C.;
RT "Chromosome and gene copy number variation allow major structural change
RT between species and strains of Leishmania.";
RL Genome Res. 21:2129-2142(2011).
RN [4] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF
RP CYS-46.
RX PubMed=18812192; DOI=10.1016/j.molbiopara.2008.08.009;
RA Sculaccio S.A., Rodrigues E.M., Cordeiro A.T., Magalhaes A., Braga A.L.,
RA Alberto E.E., Thiemann O.H.;
RT "Selenocysteine incorporation in Kinetoplastid: selenophosphate synthetase
RT (SELD) from Leishmania major and Trypanosoma brucei.";
RL Mol. Biochem. Parasitol. 162:165-171(2008).
RN [5] {ECO:0007744|PDB:5L16}
RP X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS).
RA Faim L.M., Silva I.R., Pereira H.M., Dias M.B., Silva M.T.A.,
RA Brandao-Neto J., Thiemann O.H.;
RT "Crystal Structure of N-terminus truncated selenophosphate synthetase from
RT Leishmania major.";
RL Submitted (JUL-2016) to the PDB data bank.
CC -!- FUNCTION: Synthesizes selenophosphate from selenide and ATP.
CC {ECO:0000269|PubMed:18812192}.
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:0000269|PubMed:18812192};
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:0000269|PubMed:18812192}.
CC -!- DEVELOPMENTAL STAGE: Expressed at the promastigote and amastigote
CC stages. {ECO:0000269|PubMed:15354357}.
CC -!- SIMILARITY: Belongs to the selenophosphate synthase 1 family. Class I
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG35734.3; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AF208490; AAG35734.3; ALT_INIT; mRNA.
DR EMBL; FR796432; CAJ09514.1; -; Genomic_DNA.
DR RefSeq; XP_001687128.1; XM_001687076.1.
DR PDB; 5L16; X-ray; 1.88 A; A=1-398.
DR PDBsum; 5L16; -.
DR AlphaFoldDB; Q4Q0M0; -.
DR SMR; Q4Q0M0; -.
DR STRING; 5664.LmjF.36.5410; -.
DR EnsemblProtists; CAJ09514; CAJ09514; LMJF_36_5410.
DR GeneID; 5655844; -.
DR KEGG; lma:LMJF_36_5410; -.
DR VEuPathDB; TriTrypDB:LmjF.36.5410; -.
DR VEuPathDB; TriTrypDB:LMJLV39_360066300; -.
DR VEuPathDB; TriTrypDB:LMJSD75_360066200; -.
DR eggNOG; KOG3939; Eukaryota.
DR HOGENOM; CLU_032859_1_0_1; -.
DR InParanoid; Q4Q0M0; -.
DR OMA; DNEPKYG; -.
DR BRENDA; 2.7.9.3; 2950.
DR Proteomes; UP000000542; Chromosome 36.
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; IDA:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0016260; P:selenocysteine biosynthetic process; IDA:UniProtKB.
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 PIRSF; PIRSF036407; Selenphspht_syn; 1.
DR SUPFAM; SSF55326; SSF55326; 1.
DR SUPFAM; SSF56042; SSF56042; 1.
DR TIGRFAMs; TIGR00476; selD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Selenium; Transferase.
FT CHAIN 1..398
FT /note="Selenide, water dikinase"
FT /id="PRO_0000451406"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 46
FT /evidence="ECO:0000305|PubMed:18812192"
FT BINDING 49
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 72..74
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 74
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 97
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 120
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 120
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT BINDING 171..174
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 278
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P49903"
FT SITE 49
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250|UniProtKB:P16456"
FT MUTAGEN 46
FT /note="C->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:18812192"
FT STRAND 76..83
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 89..99
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 106..122
FT /evidence="ECO:0007829|PDB:5L16"
FT TURN 123..125
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 131..142
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 144..164
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 169..179
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 181..191
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 192..194
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 198..200
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 207..212
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 216..227
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 231..236
FT /evidence="ECO:0007829|PDB:5L16"
FT TURN 237..240
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 243..258
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 262..267
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 269..271
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 276..278
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 283..294
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 304..313
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 315..323
FT /evidence="ECO:0007829|PDB:5L16"
FT TURN 324..328
FT /evidence="ECO:0007829|PDB:5L16"
FT TURN 330..333
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 342..348
FT /evidence="ECO:0007829|PDB:5L16"
FT HELIX 349..362
FT /evidence="ECO:0007829|PDB:5L16"
FT TURN 363..365
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 369..376
FT /evidence="ECO:0007829|PDB:5L16"
FT STRAND 387..397
FT /evidence="ECO:0007829|PDB:5L16"
SQ SEQUENCE 398 AA; 42687 MW; BC57C5AFD71DD20E CRC64;
MSHKRPQSSA GESNGAVDLK TPRFDPVSLG LPAEFQLTDY TRLKGCSCKL PQPKLLALLQ
ELSATPGQKD VGMDCSIVPL HHTNSKGEAL FLVSTTDFFF PSVSDPFLQG QIGAANVLSD
LYSMGIPDCD TMLMLLAAST EMDEHERLIT TREIMKGFAE RARLATTTVT GGQTVMNPWP
LIGGVAMAVV SEAEMVRPTG LLCAGDILVL TKPLGCQVAV NLKQWLLRPS PLYEEAIAGH
ISPEEIEELY NMATDSMRRL NREGARLMRK HGAHGATDVT GFGILGHANN FGAAQAVGDA
PRSLCLVLER LPMFKTAVAA SKQMNDKYRL LEGYSAETSG GLLVAFPSTT AAAAFCAELT
AVDGGCPSWI VGHVEDRATN AVDGVYARLK DGYEIVEV
