ID   SYK_CLOBM               Reviewed;         504 AA.
AC   B1KTC1;
DT   24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT   29-APR-2008, sequence version 1.
DT   03-AUG-2022, entry version 82.
DE   RecName: Full=Lysine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_00252};
DE            EC=6.1.1.6 {ECO:0000255|HAMAP-Rule:MF_00252};
DE   AltName: Full=Lysyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00252};
DE            Short=LysRS {ECO:0000255|HAMAP-Rule:MF_00252};
GN   Name=lysS {ECO:0000255|HAMAP-Rule:MF_00252}; OrderedLocusNames=CLK_2983;
OS   Clostridium botulinum (strain Loch Maree / Type A3).
OC   Bacteria; Firmicutes; Clostridia; Eubacteriales; Clostridiaceae;
OC   Clostridium.
OX   NCBI_TaxID=498214;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Loch Maree / Type A3;
RX   PubMed=18060065; DOI=10.1371/journal.pone.0001271;
RA   Smith T.J., Hill K.K., Foley B.T., Detter J.C., Munk A.C., Bruce D.C.,
RA   Doggett N.A., Smith L.A., Marks J.D., Xie G., Brettin T.S.;
RT   "Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4
RT   and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within
RT   plasmids.";
RL   PLoS ONE 2:E1271-E1271(2007).
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         Evidence={ECO:0000255|HAMAP-Rule:MF_00252};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00252};
CC       Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000255|HAMAP-
CC       Rule:MF_00252};
CC   -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00252}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00252}.
CC   -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00252}.
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DR   EMBL; CP000962; ACA54800.1; -; Genomic_DNA.
DR   RefSeq; WP_012342857.1; NC_010520.1.
DR   AlphaFoldDB; B1KTC1; -.
DR   SMR; B1KTC1; -.
DR   EnsemblBacteria; ACA54800; ACA54800; CLK_2983.
DR   KEGG; cbl:CLK_2983; -.
DR   HOGENOM; CLU_008255_6_0_9; -.
DR   OMA; EIFGEKC; -.
DR   Proteomes; UP000000722; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0004824; F:lysine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR   GO; GO:0006430; P:lysyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
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   3: Inferred from homology;
KW   Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase; Magnesium;
KW   Metal-binding; Nucleotide-binding; Protein biosynthesis.
FT   CHAIN           1..504
FT                   /note="Lysine--tRNA ligase"
FT                   /id="PRO_1000101112"
FT   BINDING         411
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00252"
FT   BINDING         418
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00252"
FT   BINDING         418
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00252"
SQ   SEQUENCE   504 AA;  58271 MW;  68BB16DD83903C11 CRC64;
     MSKEDNVINN FEEQANELMK ERFQKLKELQ SNGKDPFDVY KVERTHTSKE VKDNYEDLEG
     KTVTVAGRLM SKRVHGKAGF SDIHDRYGKI QLYIKINDVG EEKLKEYKTF DIGDIISVTG
     TVFKTKTGET SIHITDFQLV CKSLRPLPEK WHGLKDPDLR YRQRYVDLII NQDVRDTFIK
     RTAIIKSMRE FLDNRGFLEV ETPILSPIAG GAAAKPFITH HNALDIDMYL RIATELYLKR
     LIVGGFEKVY EIGKNFRNEG IDIRHNPEFT AIELYEAYAD YNDMMEITEN MIAYICEKVL
     GTTKVEYEGA EIDFTPPWRR LTMVDAVKEY AGVDFNIIKD DIEARAIAKE KHIEFKKELK
     DCTKGDVLIG LFEEFCEDKL MQPTFICDYP VENSPLTKKK RGNEAFTERF EGFVFGREVC
     NAYSELNDSI VQKERFMQQL KERELGDDEA YMMDDDFITS LEVGMPPTGG LGIGIDRLIM
     FLTDTHSIRD VILFPTMKPQ PNNQ