SPCS_METMP
ID SPCS_METMP Reviewed; 436 AA.
AC Q6LZM9;
DT 29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 94.
DE RecName: Full=O-phosphoseryl-tRNA(Sec) selenium transferase;
DE EC=2.9.1.2 {ECO:0000269|PubMed:17142313};
DE AltName: Full=Selenocysteine synthase;
DE Short=Sec synthase;
DE AltName: Full=Selenocysteinyl-tRNA(Sec) synthase;
DE AltName: Full=Sep-tRNA:Sec-tRNA synthase;
DE Short=SepSecS;
GN Name=spcS; OrderedLocusNames=MMP0595;
OS Methanococcus maripaludis (strain S2 / LL).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanococcaceae; Methanococcus.
OX NCBI_TaxID=267377;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S2 / LL;
RX PubMed=15466049; DOI=10.1128/jb.186.20.6956-6969.2004;
RA Hendrickson E.L., Kaul R., Zhou Y., Bovee D., Chapman P., Chung J.,
RA Conway de Macario E., Dodsworth J.A., Gillett W., Graham D.E., Hackett M.,
RA Haydock A.K., Kang A., Land M.L., Levy R., Lie T.J., Major T.A.,
RA Moore B.C., Porat I., Palmeiri A., Rouse G., Saenphimmachak C., Soell D.,
RA Van Dien S., Wang T., Whitman W.B., Xia Q., Zhang Y., Larimer F.W.,
RA Olson M.V., Leigh J.A.;
RT "Complete genome sequence of the genetically tractable hydrogenotrophic
RT methanogen Methanococcus maripaludis.";
RL J. Bacteriol. 186:6956-6969(2004).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, PYRIDOXAL PHOSPHATE AT LYS-278, AND
RP MUTAGENESIS OF LYS-278.
RX PubMed=17142313; DOI=10.1073/pnas.0609703104;
RA Yuan J., Palioura S., Salazar J.C., Su D., O'Donoghue P., Hohn M.J.,
RA Cardoso A.M., Whitman W.B., Soell D.;
RT "RNA-dependent conversion of phosphoserine forms selenocysteine in
RT eukaryotes and archaea.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:18923-18927(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE,
RP SUBUNIT, AND MUTAGENESIS OF ARG-72; ARG-94; ASN-247 AND ARG-307.
RX PubMed=18158303; DOI=10.1093/nar/gkm1122;
RA Araiso Y., Palioura S., Ishitani R., Sherrer R.L., O'Donoghue P., Yuan J.,
RA Oshikane H., Domae N., Defranco J., Soll D., Nureki O.;
RT "Structural insights into RNA-dependent eukaryal and archaeal
RT selenocysteine formation.";
RL Nucleic Acids Res. 36:1187-1199(2008).
CC -!- FUNCTION: Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-
CC tRNA(Sec) required for selenoprotein biosynthesis.
CC {ECO:0000269|PubMed:17142313}.
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:0000269|PubMed:17142313};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:18158303};
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:0000269|PubMed:17142313}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:18158303}.
CC -!- SIMILARITY: Belongs to the SepSecS family. {ECO:0000305}.
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DR EMBL; BX950229; CAF30151.1; -; Genomic_DNA.
DR RefSeq; WP_011170539.1; NC_005791.1.
DR PDB; 2Z67; X-ray; 2.50 A; A/B/C/D=1-436.
DR PDBsum; 2Z67; -.
DR AlphaFoldDB; Q6LZM9; -.
DR SMR; Q6LZM9; -.
DR STRING; 267377.MMP0595; -.
DR EnsemblBacteria; CAF30151; CAF30151; MMP0595.
DR GeneID; 2762564; -.
DR KEGG; mmp:MMP0595; -.
DR PATRIC; fig|267377.15.peg.609; -.
DR eggNOG; arCOG00119; Archaea.
DR HOGENOM; CLU_022508_0_0_2; -.
DR OMA; HIINGAY; -.
DR OrthoDB; 16805at2157; -.
DR BioCyc; MetaCyc:MON-14963; -.
DR BioCyc; MMAR267377:MMP_RS03135-MON; -.
DR BRENDA; 2.9.1.2; 3262.
DR UniPathway; UPA00906; UER00898.
DR EvolutionaryTrace; Q6LZM9; -.
DR Proteomes; UP000000590; Chromosome.
DR GO; GO:0098621; F:phosphoseryl-selenocysteinyl-tRNA selenium transferase activity; IEA:UniProtKB-EC.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0097056; P:selenocysteinyl-tRNA(Sec) biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
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; 1.
DR PIRSF; PIRSF017689; SepSecS; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR03531; selenium_SpcS; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Protein biosynthesis; Pyridoxal phosphate;
KW Reference proteome; RNA-binding; Selenium; Transferase; tRNA-binding.
FT CHAIN 1..436
FT /note="O-phosphoseryl-tRNA(Sec) selenium transferase"
FT /id="PRO_0000219883"
FT REGION 1..44
FT /note="Tetramerization"
FT /evidence="ECO:0000250|UniProtKB:Q6P6M7"
FT REGION 93..103
FT /note="Phosphate loop (P-loop)"
FT /evidence="ECO:0000250|UniProtKB:Q6P6M7"
FT BINDING 72
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:18158303"
FT BINDING 94
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18158303"
FT BINDING 95
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18158303"
FT BINDING 102
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18158303"
FT BINDING 307
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18158303"
FT SITE 71
FT /note="May act as a substrate filter by repelling compounds
FT with a negatively charged alpha-carboxylate"
FT /evidence="ECO:0000250"
FT MOD_RES 278
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:17142313,
FT ECO:0000269|PubMed:18158303"
FT MUTAGEN 72
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:18158303"
FT MUTAGEN 94
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:18158303"
FT MUTAGEN 247
FT /note="N->A: Reduced activity."
FT /evidence="ECO:0000269|PubMed:18158303"
FT MUTAGEN 278
FT /note="K->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17142313"
FT MUTAGEN 307
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:18158303"
FT STRAND 8..10
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 12..25
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 27..35
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 45..56
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 60..62
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 79..84
FT /evidence="ECO:0007829|PDB:2Z67"
FT TURN 85..87
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 106..125
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 131..137
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 139..154
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 158..162
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 167..175
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 179..183
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 186..188
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 196..208
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 213..220
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 230..240
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 244..247
FT /evidence="ECO:0007829|PDB:2Z67"
FT TURN 249..253
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 255..265
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 270..275
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 276..280
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 287..292
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 294..301
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 311..352
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 363..369
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 374..383
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 386..388
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 390..392
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 397..400
FT /evidence="ECO:0007829|PDB:2Z67"
FT STRAND 410..414
FT /evidence="ECO:0007829|PDB:2Z67"
FT HELIX 421..432
FT /evidence="ECO:0007829|PDB:2Z67"
SQ SEQUENCE 436 AA; 48447 MW; 6B7CB252D5ABE6A0 CRC64;
MLDFNIEGLI PKNMEKRGEL VLNEYLKEIE DVFNHRKIPE NGIDDEKIKL FLKFLSMMDT
DKDPKSVRIG EREARTYSKI HEELSSGFCH GIGRSGNLVD PQPKASGASI MYALTNKILE
SFFKQLGLNV HAIATPISTG MSISLCLSAA RKKYGSNVVI YPYASHKSPI KAVSFVGMNM
RLVETVLDGD RVYVPVEDIE NAIKKEIELG NRPCVLSTLT FFPPRNSDDI VEIAKICENY
DIPHIINGAY AIQNNYYLEK LKKAFKYRVD AVVSSSDKNL LTPIGGGLVY STDAEFIKEI
SLSYPGRASA TPVVNTLVSL LSMGSKNYLE LVKNQKNSKK LLDELLNDLS KKTGGKFLDV
ESPIASCISV NSDPVEIAAK LYNLRVTGPR GIKKTDHFGN CYLGTYTHDY IVMNAAIGVR
TEDIVNSVSK LEKILL
