SYKC_YEAST
ID SYKC_YEAST Reviewed; 591 AA.
AC P15180; D6VS25;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 206.
DE RecName: Full=Lysine--tRNA ligase, cytoplasmic;
DE EC=6.1.1.6;
DE AltName: Full=Lysyl-tRNA synthetase;
DE Short=LysRS;
GN Name=KRS1; Synonyms=GCD5; OrderedLocusNames=YDR037W; ORFNames=YD9673.09;
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], AND PROTEIN SEQUENCE OF 58-77.
RC STRAIN=ATCC 26109 / X2180;
RX PubMed=2903861; DOI=10.1016/s0021-9258(19)81378-9;
RA Mirande M., Waller J.-P.;
RT "The yeast lysyl-tRNA synthetase gene. Evidence for general amino acid
RT control of its expression and domain structure of the encoded protein.";
RL J. Biol. Chem. 263:18443-18451(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=7305B;
RX PubMed=2046655; DOI=10.1007/bf00260720;
RA Martinez R., Latreille M.-T., Mirande M.;
RT "A PMR2 tandem repeat with a modified C-terminus is located downstream from
RT the KRS1 gene encoding lysyl-tRNA synthetase in Saccharomyces cerevisiae.";
RL Mol. Gen. Genet. 227:149-154(1991).
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 PARTIAL NUCLEOTIDE SEQUENCE, AND MUTAGENESIS OF ARG-488.
RX PubMed=1505029; DOI=10.1016/0092-8674(92)90433-d;
RA Lanker S., Bushman J.L., Hinnebusch A.G., Trachsel H., Mueller P.P.;
RT "Autoregulation of the yeast lysyl-tRNA synthetase gene GCD5/KRS1 by
RT translational and transcriptional control mechanisms.";
RL Cell 70:647-657(1992).
RN [6]
RP PROTEIN SEQUENCE OF 178-188.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7895733; DOI=10.1002/elps.11501501210;
RA Garrels J.I., Futcher B., Kobayashi R., Latter G.I., Schwender B.,
RA Volpe T., Warner J.R., McLaughlin C.S.;
RT "Protein identifications for a Saccharomyces cerevisiae protein database.";
RL Electrophoresis 15:1466-1486(1994).
RN [7]
RP ACETYLATION AT SER-2.
RX PubMed=9298649; DOI=10.1002/elps.1150180810;
RA Garrels J.I., McLaughlin C.S., Warner J.R., Futcher B., Latter G.I.,
RA Kobayashi R., Schwender B., Volpe T., Anderson D.S., Mesquita-Fuentes R.,
RA Payne W.E.;
RT "Proteome studies of Saccharomyces cerevisiae: identification and
RT characterization of abundant proteins.";
RL Electrophoresis 18:1347-1360(1997).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-62, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-62, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-30 AND THR-62, AND
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 [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-62, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [12]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-308 AND LYS-577, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22106047; DOI=10.1002/pmic.201100166;
RA Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL Proteomics 12:236-240(2012).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-
CC tRNA(Lys); Xref=Rhea:RHEA:20792, Rhea:RHEA-COMP:9696, Rhea:RHEA-
CC COMP:9697, ChEBI:CHEBI:30616, ChEBI:CHEBI:32551, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78529, ChEBI:CHEBI:456215; EC=6.1.1.6;
CC -!- SUBUNIT: Homodimer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
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DR EMBL; J04186; AAA66916.1; -; Genomic_DNA.
DR EMBL; X56259; CAA39699.1; -; Genomic_DNA.
DR EMBL; Z68196; CAA92376.1; -; Genomic_DNA.
DR EMBL; Z74333; CAA98863.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11885.1; -; Genomic_DNA.
DR PIR; A92695; SYBYKT.
DR RefSeq; NP_010322.1; NM_001180345.1.
DR AlphaFoldDB; P15180; -.
DR SMR; P15180; -.
DR BioGRID; 32092; 164.
DR DIP; DIP-6359N; -.
DR IntAct; P15180; 10.
DR MINT; P15180; -.
DR STRING; 4932.YDR037W; -.
DR CarbonylDB; P15180; -.
DR iPTMnet; P15180; -.
DR MaxQB; P15180; -.
DR PaxDb; P15180; -.
DR PRIDE; P15180; -.
DR EnsemblFungi; YDR037W_mRNA; YDR037W; YDR037W.
DR GeneID; 851607; -.
DR KEGG; sce:YDR037W; -.
DR SGD; S000002444; KRS1.
DR VEuPathDB; FungiDB:YDR037W; -.
DR eggNOG; KOG1885; Eukaryota.
DR GeneTree; ENSGT01030000234618; -.
DR HOGENOM; CLU_008255_6_0_1; -.
DR InParanoid; P15180; -.
DR OMA; EIFGEKC; -.
DR BioCyc; YEAST:G3O-29651-MON; -.
DR PRO; PR:P15180; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P15180; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004824; F:lysine-tRNA ligase activity; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; HDA:SGD.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IDA:SGD.
DR CDD; cd00775; LysRS_core; 1.
DR CDD; cd04322; LysRS_N; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_00252; Lys_tRNA_synth_class2; 1.
DR InterPro; IPR004364; Aa-tRNA-synt_II.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR002313; Lys-tRNA-ligase_II.
DR InterPro; IPR034762; Lys-tRNA-ligase_II_bac/euk.
DR InterPro; IPR044136; Lys-tRNA-ligase_II_N.
DR InterPro; IPR018149; Lys-tRNA-synth_II_C.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004365; NA-bd_OB_tRNA.
DR Pfam; PF00152; tRNA-synt_2; 1.
DR Pfam; PF01336; tRNA_anti-codon; 1.
DR PIRSF; PIRSF039101; LysRS2; 1.
DR PRINTS; PR00982; TRNASYNTHLYS.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00499; lysS_bact; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW Acetylation; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW Direct protein sequencing; Isopeptide bond; Ligase; Nucleotide-binding;
KW Phosphoprotein; Protein biosynthesis; Reference proteome; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9298649"
FT CHAIN 2..591
FT /note="Lysine--tRNA ligase, cytoplasmic"
FT /id="PRO_0000152771"
FT REGION 1..64
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 24..49
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000269|PubMed:9298649"
FT MOD_RES 30
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 62
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17287358,
FT ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT CROSSLNK 308
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT CROSSLNK 577
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT MUTAGEN 488
FT /note="R->L: In GCD5-1; defects in lysine-binding."
FT /evidence="ECO:0000269|PubMed:1505029"
FT CONFLICT 22
FT /note="A -> V (in Ref. 2; CAA39699)"
FT /evidence="ECO:0000305"
FT CONFLICT 51
FT /note="A -> T (in Ref. 2; CAA39699)"
FT /evidence="ECO:0000305"
FT CONFLICT 111
FT /note="A -> V (in Ref. 2; CAA39699)"
FT /evidence="ECO:0000305"
FT CONFLICT 162
FT /note="C -> H (in Ref. 2; CAA39699)"
FT /evidence="ECO:0000305"
FT CONFLICT 165
FT /note="D -> E (in Ref. 2; CAA39699)"
FT /evidence="ECO:0000305"
FT CONFLICT 259
FT /note="R -> K (in Ref. 2; CAA39699)"
FT /evidence="ECO:0000305"
FT CONFLICT 430..432
FT /note="ILV -> VLA (in Ref. 2; CAA39699)"
FT /evidence="ECO:0000305"
FT CONFLICT 591
FT /note="N -> H (in Ref. 2; CAA39699)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 591 AA; 67959 MW; 3CFBC6EC396B1CCF CRC64;
MSQQDNVKAA AEGVANLHLD EATGEMVSKS ELKKRIKQRQ VEAKKAAKKA AAQPKPASKK
KTDLFADLDP SQYFETRSRQ IQELRKTHEP NPYPHKFHVS ISNPEFLAKY AHLKKGETLP
EEKVSIAGRI HAKRESGSKL KFYVLHGDGV EVQLMSQLQD YCDPDSYEKD HDLLKRGDIV
GVEGYVGRTQ PKKGGEGEVS VFVSRVQLLT PCLHMLPADH FGFKDQETRY RKRYLDLIMN
KDARNRFITR SEIIRYIRRF LDQRKFIEVE TPMMNVIAGG ATAKPFITHH NDLDMDMYMR
IAPELFLKQL VVGGLDRVYE IGRQFRNEGI DMTHNPEFTT CEFYQAYADV YDLMDMTELM
FSEMVKEITG SYIIKYHPDP ADPAKELELN FSRPWKRINM IEELEKVFNV KFPSGDQLHT
AETGEFLKKI LVDNKLECPP PLTNARMLDK LVGELEDTCI NPTFIFGHPQ MMSPLAKYSR
DQPGLCERFE VFVATKEICN AYTELNDPFD QRARFEEQAR QKDQGDDEAQ LVDETFCNAL
EYGLPPTGGW GCGIDRLAMF LTDSNTIREV LLFPTLKPDV LREEVKKEEE N
