ID   SYK_THIDA               Reviewed;         501 AA.
AC   Q3SKD9;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   11-OCT-2005, sequence version 1.
DT   03-AUG-2022, entry version 113.
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=Tbd_0893;
OS   Thiobacillus denitrificans (strain ATCC 25259).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Nitrosomonadales;
OC   Thiobacillaceae; Thiobacillus.
OX   NCBI_TaxID=292415;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25259;
RX   PubMed=16452431; DOI=10.1128/jb.188.4.1473-1488.2006;
RA   Beller H.R., Chain P.S., Letain T.E., Chakicherla A., Larimer F.W.,
RA   Richardson P.M., Coleman M.A., Wood A.P., Kelly D.P.;
RT   "The genome sequence of the obligately chemolithoautotrophic, facultatively
RT   anaerobic bacterium Thiobacillus denitrificans.";
RL   J. Bacteriol. 188:1473-1488(2006).
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; CP000116; AAZ96846.1; -; Genomic_DNA.
DR   RefSeq; WP_011311405.1; NC_007404.1.
DR   AlphaFoldDB; Q3SKD9; -.
DR   SMR; Q3SKD9; -.
DR   STRING; 292415.Tbd_0893; -.
DR   PRIDE; Q3SKD9; -.
DR   EnsemblBacteria; AAZ96846; AAZ96846; Tbd_0893.
DR   KEGG; tbd:Tbd_0893; -.
DR   eggNOG; COG1190; Bacteria.
DR   HOGENOM; CLU_008255_6_0_4; -.
DR   OMA; EIFGEKC; -.
DR   OrthoDB; 63621at2; -.
DR   Proteomes; UP000008291; 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; 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   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;
KW   Reference proteome.
FT   CHAIN           1..501
FT                   /note="Lysine--tRNA ligase"
FT                   /id="PRO_1000199251"
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   501 AA;  56921 MW;  BD09D19431FDA754 CRC64;
     MTDPTNAPAL DENQIIAERR AKLAAIREAG VAFPNDFERR DYAGRLAHEH GDKSKEALEA
     EAVDVQLAGR MMLKRVMGKA SFATLQDMSG RIQVYVSNDL TGLDAHEAFK RWDLGDFVGV
     SGTLFKTNKG ELTIQAKSVR LLSKALRPLP EKFHGLADQE QKYRQRYLDL ITNDDARSTF
     VRRSKIIQAI REFMTGHGFL EVETPMMHPI PGGAAAKPFV THHNALDMEL FLRIAPELYL
     KRLVVGGFEK VFEINRNFRN EGLSTRHNPE FTMMEFYEAY REYRYLMDFT EALIRHTAVA
     ATGSTTISYQ GSTIELGTPF DRLTIVEAVR KYHPEYTVEQ LNDRDWLTAQ FTAMKAKYRE
     HDGLGGLQLT FFEETTEALL VQPTFIVDYP AEVSPLARRS DTQPEITERF ELFITGREMA
     NGFSELNDAE DQAERFMEQV RAKEAGDEEA MHYDADFIRA LEHGLPPTGG CGIGIDRLVM
     LLTDSPSIRD VILFPQMRRE A