SPCS_LEIDO
ID SPCS_LEIDO Reviewed; 595 AA.
AC A0A3S7WQS5;
DT 12-AUG-2020, integrated into UniProtKB/Swiss-Prot.
DT 08-MAY-2019, sequence version 1.
DT 03-AUG-2022, entry version 14.
DE RecName: Full=O-phosphoseryl-tRNA(Sec) selenium transferase {ECO:0000255|PIRNR:PIRNR017689};
DE EC=2.9.1.2 {ECO:0000255|PIRNR:PIRNR017689, ECO:0000269|PubMed:26586914};
DE AltName: Full=Selenocysteine synthase {ECO:0000255|PIRNR:PIRNR017689};
DE AltName: Full=Selenocysteinyl-tRNA(Sec) synthase {ECO:0000255|PIRNR:PIRNR017689, ECO:0000303|PubMed:26586914};
DE AltName: Full=Sep-tRNA:Sec-tRNA synthase {ECO:0000255|PIRNR:PIRNR017689};
GN Name=SepSecS {ECO:0000303|PubMed:26586914};
GN ORFNames=LdCL_090015500 {ECO:0000312|EMBL:AYU76541.1};
OS Leishmania donovani.
OC Eukaryota; Discoba; Euglenozoa; Kinetoplastea; Metakinetoplastina;
OC Trypanosomatida; Trypanosomatidae; Leishmaniinae; Leishmania.
OX NCBI_TaxID=5661 {ECO:0000312|Proteomes:UP000274082};
RN [1] {ECO:0000312|Proteomes:UP000274082}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LdCL {ECO:0000312|Proteomes:UP000274082};
RX PubMed=30409989; DOI=10.1038/s41598-018-34812-x;
RA Lypaczewski P., Hoshizaki J., Zhang W.-W., McCall L.-I.,
RA Torcivia-Rodriguez J., Simonyan V., Kaur A., Dewar K., Matlashewski G.;
RT "A complete Leishmania donovani reference genome identifies novel genetic
RT variations associated with virulence.";
RL Sci. Rep. 8:16549-16549(2018).
RN [2] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, SUBUNIT, SUBCELLULAR LOCATION,
RP DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RC STRAIN=MHOM/SD/62/1SCL2D {ECO:0000269|PubMed:26586914};
RX PubMed=26586914; DOI=10.1074/jbc.m115.695007;
RA Manhas R., Gowri V.S., Madhubala R.;
RT "Leishmania donovani Encodes a Functional Selenocysteinyl-tRNA Synthase.";
RL J. Biol. Chem. 291:1203-1220(2016).
CC -!- FUNCTION: Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-
CC tRNA(Sec) required for selenoprotein biosynthesis.
CC {ECO:0000255|PIRNR:PIRNR017689, ECO:0000269|PubMed:26586914}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + O-phospho-L-seryl-tRNA(Sec) + selenophosphate = L-
CC selenocysteinyl-tRNA(Sec) + 2 phosphate; Xref=Rhea:RHEA:25041,
CC Rhea:RHEA-COMP:9743, Rhea:RHEA-COMP:9947, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:16144, ChEBI:CHEBI:43474, ChEBI:CHEBI:78551,
CC ChEBI:CHEBI:78573; EC=2.9.1.2;
CC Evidence={ECO:0000255|PIRNR:PIRNR017689,
CC ECO:0000269|PubMed:26586914};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|PIRNR:PIRNR017689,
CC ECO:0000255|PIRSR:PIRSR017689-50};
CC -!- PATHWAY: Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec)
CC biosynthesis; selenocysteinyl-tRNA(Sec) from L-seryl-tRNA(Sec)
CC (archaeal/eukaryal route): step 2/2. {ECO:0000255|PIRNR:PIRNR017689,
CC ECO:0000269|PubMed:26586914}.
CC -!- SUBUNIT: Homotetramer composed of two homodimers.
CC {ECO:0000269|PubMed:26586914}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|PIRNR:PIRNR017689,
CC ECO:0000269|PubMed:26586914}.
CC -!- DEVELOPMENTAL STAGE: Expressed at the promastigote stage.
CC {ECO:0000269|PubMed:26586914}.
CC -!- DISRUPTION PHENOTYPE: Impaired selenocysteine incorporation into
CC proteins, such as SelT, SelK and SelTryp (PubMed:26586914). No defect
CC in promastigote growth rate and in their capacity to infect host
CC macrophages (PubMed:26586914). {ECO:0000269|PubMed:26586914}.
CC -!- SIMILARITY: Belongs to the SepSecS family.
CC {ECO:0000255|PIRNR:PIRNR017689}.
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DR EMBL; CP029508; AYU76541.1; -; Genomic_DNA.
DR RefSeq; XP_003858779.1; XM_003858731.1.
DR AlphaFoldDB; A0A3S7WQS5; -.
DR SMR; A0A3S7WQS5; -.
DR GeneID; 13392061; -.
DR KEGG; ldo:LDBPK_091000; -.
DR VEuPathDB; TriTrypDB:LdBPK_091000.1; -.
DR VEuPathDB; TriTrypDB:LdCL_090015500; -.
DR VEuPathDB; TriTrypDB:LDHU3_09.1170; -.
DR OMA; MDTNNFA; -.
DR UniPathway; UPA00906; UER00898.
DR Proteomes; UP000274082; Chromosome ldcl_09.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0098621; F:phosphoseryl-selenocysteinyl-tRNA selenium transferase activity; IEA:UniProtKB-EC.
DR GO; GO:0016785; F:selenotransferase activity; IDA:UniProtKB.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0097056; P:selenocysteinyl-tRNA(Sec) biosynthetic process; IDA:UniProtKB.
DR GO; GO:0006412; P:translation; IDA:UniProtKB.
DR Gene3D; 3.40.640.10; -; 1.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR019872; Sec-tRNA_Se_transferase.
DR InterPro; IPR008829; SepSecS/SepCysS.
DR PANTHER; PTHR12944; PTHR12944; 1.
DR Pfam; PF05889; SepSecS; 2.
DR PIRSF; PIRSF017689; SepSecS; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Protein biosynthesis; Pyridoxal phosphate; RNA-binding;
KW Selenium; Transferase; tRNA-binding.
FT CHAIN 1..595
FT /note="O-phosphoseryl-tRNA(Sec) selenium transferase"
FT /id="PRO_0000450616"
FT REGION 96..106
FT /note="Phosphate loop (P-loop)"
FT /evidence="ECO:0000250|UniProtKB:Q9HD40"
FT REGION 174..208
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 257..278
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 174..189
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 75
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|PIRSR:PIRSR017689-50"
FT BINDING 97
FT /ligand="substrate"
FT /evidence="ECO:0000255|PIRSR:PIRSR017689-50"
FT BINDING 98
FT /ligand="substrate"
FT /evidence="ECO:0000255|PIRSR:PIRSR017689-50"
FT BINDING 105
FT /ligand="substrate"
FT /evidence="ECO:0000255|PIRSR:PIRSR017689-50"
FT BINDING 358
FT /ligand="tRNA"
FT /ligand_id="ChEBI:CHEBI:17843"
FT /ligand_part="tRNA variable arm"
FT /evidence="ECO:0000255|PIRSR:PIRSR017689-50"
FT BINDING 400
FT /ligand="substrate"
FT /evidence="ECO:0000255|PIRSR:PIRSR017689-50"
FT SITE 74
FT /note="May act as a substrate filter by repelling compounds
FT with a negatively charged alpha-carboxylate"
FT /evidence="ECO:0000255|PIRSR:PIRSR017689-50"
FT MOD_RES 371
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|PIRSR:PIRSR017689-50"
SQ SEQUENCE 595 AA; 63923 MW; FA49E5C1184CC3C6 CRC64;
MDDRSLKLAE DFVSARYIEA GRESLRATAR IMRSILAQRC CPDEGLTDAA IELILRQLSL
MDTNNLAHHV GGGEREGRVV SALVRMRHFH LTHGIGRSGD LFSEQPKAAG SSLLYKITNV
LMLDLIRQAG APSTAAAVVV PMATGMTLAL VLRCVAKTHM KELMKEAEAV QLQRTVTKDS
TSATSAAPVQ EPPMSEADRD RHDRTSLPVP ATPRYVIWPR IDQKTALKCI DAAGLVPVPV
QLRPAVPLAR SAAPCVSTNR DSLDRGQDSI GSPSTPTSSS SLFLECHVDD VAAAVNAVGG
PSQVVCVLST TSCFAPRLPD NTVAIAQYCK KAGIPYVVNN AYGVQSRRIM TRLDAAQRLG
RVDFVVQSGD KNFLVPVGGS IICSGDKERC KAVAALYAGR ASMSPIVDLF ITALSLGRRG
MQTLWSDRYK CRARLIRQLR VFARERREVL LVDDSDDDKA DEDTVGGSQR TSNAVVPRND
ISVAVTMRAY GLPAAEASSS GAQLGSEQAG RVTNWAAARA LGAQLFRSAV TGPRVITPAP
STPTTIAGCT FRNYGMHQDR EPPCPLLVIA CGIGMSESEV DALMARLRDL WPVPA
