ID   SYK_ONYPE               Reviewed;         511 AA.
AC   Q6YPY6;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 115.
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}; Synonyms=pam589;
GN   OrderedLocusNames=PAM_589;
OS   Onion yellows phytoplasma (strain OY-M).
OC   Bacteria; Tenericutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae;
OC   Candidatus Phytoplasma; Candidatus Phytoplasma asteris.
OX   NCBI_TaxID=262768;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=OY-M;
RX   PubMed=14661021; DOI=10.1038/ng1277;
RA   Oshima K., Kakizawa S., Nishigawa H., Jung H.-Y., Wei W., Suzuki S.,
RA   Arashida R., Nakata D., Miyata S., Ugaki M., Namba S.;
RT   "Reductive evolution suggested from the complete genome sequence of a
RT   plant-pathogenic phytoplasma.";
RL   Nat. Genet. 36:27-29(2004).
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; AP006628; BAD04674.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q6YPY6; -.
DR   SMR; Q6YPY6; -.
DR   STRING; 262768.PAM_589; -.
DR   EnsemblBacteria; BAD04674; BAD04674; PAM_589.
DR   KEGG; poy:PAM_589; -.
DR   eggNOG; COG1190; Bacteria.
DR   HOGENOM; CLU_008255_6_0_14; -.
DR   OMA; EIFGEKC; -.
DR   OrthoDB; 63621at2; -.
DR   BioCyc; OYEL262768:G1G26-714-MON; -.
DR   Proteomes; UP000002523; 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..511
FT                   /note="Lysine--tRNA ligase"
FT                   /id="PRO_1000199246"
FT   BINDING         403
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00252"
FT   BINDING         410
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00252"
FT   BINDING         410
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00252"
SQ   SEQUENCE   511 AA;  58722 MW;  E8662630D1139521 CRC64;
     MATKLSEQEI IRHQKMNELK KINIDPFGKK FVPSHSIEQI LLQYQKADSL ALEQSQIHVC
     VAGRIVLKRG QGKAGFLHLQ DFNFRMQAYI KLDLVGKDAF QIYQNCDLGD IIGIKGFLFK
     TKTQELTIKA LEFIHLTKAL KPLPDKFHGL QNREEMRKNR YVDLIVNEKT RQVFLTRSLI
     MKYIRNFFDN QGFLEVETPI LQPTLGGASA KPFITHHNAL NCDFYLRIAT ELPLKKLIVG
     GMNKVYEIGR LFRNEGIDAT HNPEFSTIEA YLAYADMQDI MDLTKQCLQE LAQKLFGKLQ
     FTYQNQEIDF SHFAKVSMVA SIKEKTGIDF TDNFTLEQCL SLAKKHQIEV MPHFSQGHII
     EAFFGKYVEN TLIQPTFVYG HPLEISPLAK QNEADPRFTD RFELFIVGKE FANAFSELND
     PIEQEKRFLN QLQQKQLGND EANDMDYDFL NALNYGMPPT GGLGMGLDRL VMLLTDTANI
     RDVILFPHCK NQNKFSQNKT ANKVLTNNDN E