ID SYSC_YEAST Reviewed; 462 AA.
AC P07284; D6VS09;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 27-MAR-2024, entry version 199.
DE RecName: Full=Serine--tRNA ligase, cytoplasmic {ECO:0000305};
DE EC=6.1.1.11 {ECO:0000269|PubMed:3031581};
DE AltName: Full=Seryl-tRNA synthetase {ECO:0000303|PubMed:3031581};
DE Short=SerRS;
DE AltName: Full=Seryl-tRNA(Ser) synthetase {ECO:0000305};
GN Name=SES1; Synonyms=SERS {ECO:0000303|PubMed:3031581};
GN OrderedLocusNames=YDR023W; ORFNames=YD9813.01;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 5-9 AND 182-190,
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=3031581; DOI=10.1093/nar/15.5.1887;
RA Weygand-Durasevic I., Johnson-Burke D., Soell D.;
RT "Cloning and characterization of the gene coding for cytoplasmic seryl-tRNA
RT synthetase from Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 15:1887-1904(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8896275;
RX DOI=10.1002/(sici)1097-0061(199609)12:10b<1085::aid-yea9>3.3.co;2-s;
RA Eide L.G., Sander C., Prydz H.;
RT "Sequencing and analysis of a 35.4 kb region on the right arm of chromosome
RT IV from Saccharomyces cerevisiae reveal 23 open reading frames.";
RL Yeast 12:1085-1090(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 451-462.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8070651; DOI=10.1093/genetics/137.2.369;
RA Folley L.S., Fox T.D.;
RT "Reduced dosage of genes encoding ribosomal protein S18 suppresses a
RT mitochondrial initiation codon mutation in Saccharomyces cerevisiae.";
RL Genetics 137:369-379(1994).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [8]
RP INTERACTION WITH ABP140.
RX PubMed=28003514; DOI=10.1261/rna.059667.116;
RA Han L., Marcus E., D'Silva S., Phizicky E.M.;
RT "S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine
RT modification of the anticodon loop of tRNA substrates.";
RL RNA 23:406-419(2017).
CC -!- FUNCTION: Catalyzes the attachment of serine to tRNA(Ser) in a two-step
CC reaction: serine is first activated by ATP to form Ser-AMP and then
CC transferred to the acceptor end of tRNA(Ser).
CC {ECO:0000269|PubMed:3031581}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-
CC seryl-tRNA(Ser); Xref=Rhea:RHEA:12292, Rhea:RHEA-COMP:9669,
CC Rhea:RHEA-COMP:9703, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:33384, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78533, ChEBI:CHEBI:456215; EC=6.1.1.11;
CC Evidence={ECO:0000269|PubMed:3031581};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:12293;
CC Evidence={ECO:0000269|PubMed:3031581};
CC -!- SUBUNIT: Homodimer; the tRNA molecule probably binds across the dimer
CC (PubMed:3031581). Interacts with ABP140; interaction is required for
CC the tRNA N(3)-methylcytidine methyltransferase activity of ABP140
CC (PubMed:28003514). {ECO:0000269|PubMed:28003514,
CC ECO:0000269|PubMed:3031581}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
CC {ECO:0000250|UniProtKB:P49591}.
CC -!- DOMAIN: Consists of two distinct domains, a catalytic core and a N-
CC terminal extension that is involved in tRNA binding.
CC {ECO:0000250|UniProtKB:P49591}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC Type-1 seryl-tRNA synthetase subfamily. {ECO:0000305}.
CC -!- CAUTION: Although this enzyme participates in the selenocysteinyl-
CC tRNA(Sec) biosynthesis pathway in many taxa, this pathway has been
CC shown in PubMed:30742068 to be lost in dikarya. {ECO:0000305}.
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DR EMBL; X04884; CAA28572.1; -; Genomic_DNA.
DR EMBL; Z47814; CAA87802.1; -; Genomic_DNA.
DR EMBL; X95966; CAA65216.1; -; Genomic_DNA.
DR EMBL; Z74319; CAA98844.1; -; Genomic_DNA.
DR EMBL; L15408; AAC37412.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11869.1; -; Genomic_DNA.
DR PIR; S50930; YSBYC.
DR RefSeq; NP_010306.1; NM_001180331.1.
DR AlphaFoldDB; P07284; -.
DR SMR; P07284; -.
DR BioGRID; 32074; 75.
DR DIP; DIP-5181N; -.
DR IntAct; P07284; 11.
DR MINT; P07284; -.
DR STRING; 4932.YDR023W; -.
DR CarbonylDB; P07284; -.
DR iPTMnet; P07284; -.
DR MaxQB; P07284; -.
DR PaxDb; 4932-YDR023W; -.
DR PeptideAtlas; P07284; -.
DR EnsemblFungi; YDR023W_mRNA; YDR023W; YDR023W.
DR GeneID; 851587; -.
DR KEGG; sce:YDR023W; -.
DR AGR; SGD:S000002430; -.
DR SGD; S000002430; SES1.
DR VEuPathDB; FungiDB:YDR023W; -.
DR eggNOG; KOG2509; Eukaryota.
DR GeneTree; ENSGT00940000153792; -.
DR HOGENOM; CLU_023797_0_2_1; -.
DR InParanoid; P07284; -.
DR OMA; GYTPCFR; -.
DR OrthoDB; 239638at2759; -.
DR BioCyc; YEAST:G3O-29640-MONOMER; -.
DR BioGRID-ORCS; 851587; 10 hits in 10 CRISPR screens.
DR PRO; PR:P07284; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P07284; Protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0010494; C:cytoplasmic stress granule; HDA:SGD.
DR GO; GO:0005829; C:cytosol; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004828; F:serine-tRNA ligase activity; IDA:SGD.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0002181; P:cytoplasmic translation; ISS:UniProtKB.
DR GO; GO:0006434; P:seryl-tRNA aminoacylation; IDA:SGD.
DR CDD; cd00770; SerRS_core; 1.
DR Gene3D; 1.10.287.40; Serine-tRNA synthetase, tRNA binding domain; 1.
DR InterPro; IPR002314; aa-tRNA-synt_IIb.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR002317; Ser-tRNA-ligase_type_1.
DR InterPro; IPR015866; Ser-tRNA-synth_1_N.
DR InterPro; IPR042103; SerRS_1_N_sf.
DR InterPro; IPR033729; SerRS_core.
DR InterPro; IPR010978; tRNA-bd_arm.
DR NCBIfam; TIGR00414; serS; 1.
DR PANTHER; PTHR11778:SF7; SERINE--TRNA LIGASE, CYTOPLASMIC-RELATED; 1.
DR PANTHER; PTHR11778; SERYL-TRNA SYNTHETASE; 1.
DR Pfam; PF02403; Seryl_tRNA_N; 1.
DR Pfam; PF00587; tRNA-synt_2b; 1.
DR PIRSF; PIRSF001529; Ser-tRNA-synth_IIa; 1.
DR PRINTS; PR00981; TRNASYNTHSER.
DR SUPFAM; SSF55681; Class II aaRS and biotin synthetases; 1.
DR SUPFAM; SSF46589; tRNA-binding arm; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW Direct protein sequencing; Ligase; Nucleotide-binding;
KW Protein biosynthesis; Reference proteome.
FT CHAIN 1..462
FT /note="Serine--tRNA ligase, cytoplasmic"
FT /id="PRO_0000122199"
FT BINDING 246..248
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 279..281
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 295
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 302
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT BINDING 366..369
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 404
FT /ligand="L-serine"
FT /ligand_id="ChEBI:CHEBI:33384"
FT /evidence="ECO:0000250"
FT CONFLICT 224
FT /note="L -> P (in Ref. 1; CAA28572)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 462 AA; 53310 MW; BBED6EA47E6F547B CRC64;
MLDINQFIED KGGNPELIRQ SQKARNASVE IVDEIISDYK DWVKTRFELD ELNKKFNKLQ
KDIGLKFKNK EDASGLLAEK EKLTQQKKEL TEKEQQEDKD LKKKVFQVGN IVHPSVVVSN
DEENNELVRT WKPEDLEAVG PIASVTGKPA SLSHHEILLR LDGYDPDRGV KICGHRGYFF
RNYGVFLNQA LINYGLQFLA AKGYIPLQAP VMMNKELMSK TAQLSEFDEE LYKVIDGEDE
KYLIATSEQP ISAYHSGEWF EKPQEQLPIH YVGYSSCFRR EAGSHGKDAW GVFRVHAFEK
IEQFVITEPE KSWEEFEKMI SYSEEFYKSL KLPYRIVGIV SGELNNAAAK KYDLEAWFPY
QKEYKELVSC SNCTDYQSRN LEIRCGIKKM GDREKKYVHC LNSTLAATQR ALCCILENYQ
TEDGLVVPEV LRKYIPGEPE FLPFVNELPK NSTSSKDKKK KN
//
