ID   SYK1_ECOLI              Reviewed;         505 AA.
AC   P0A8N3; P13030; Q2M9V1;
DT   07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   27-MAR-2024, entry version 154.
DE   RecName: Full=Lysine--tRNA ligase;
DE            EC=6.1.1.6;
DE   AltName: Full=Lysyl-tRNA synthetase;
DE            Short=LysRS;
GN   Name=lysS; Synonyms=asuD, herC; OrderedLocusNames=b2890, JW2858;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=2456575; DOI=10.1073/pnas.85.15.5620;
RA   Kawakami K., Joensson Y.H., Bjoerk G.R., Ikeda H., Nakamura Y.;
RT   "Chromosomal location and structure of the operon encoding peptide-chain-
RT   release factor 2 of Escherichia coli.";
RL   Proc. Natl. Acad. Sci. U.S.A. 85:5620-5624(1988).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-28.
RX   PubMed=2183178; DOI=10.1093/nar/18.2.305;
RA   Leveque F., Plateau P., Dessen P., Blanquet S.;
RT   "Homology of lysS and lysU, the two Escherichia coli genes encoding
RT   distinct lysyl-tRNA synthetase species.";
RL   Nucleic Acids Res. 18:305-312(1990).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [5]
RP   IDENTIFICATION BY 2D-GEL.
RX   PubMed=9298644; DOI=10.1002/elps.1150180805;
RA   VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT   "Escherichia coli proteome analysis using the gene-protein database.";
RL   Electrophoresis 18:1243-1251(1997).
RN   [6]
RP   STRUCTURE BY NMR.
RX   PubMed=7473706; DOI=10.1006/jmbi.1995.0539;
RA   Commans S., Plateau P., Blanquet S., Dardel F.;
RT   "Solution structure of the anticodon-binding domain of Escherichia coli
RT   lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys).";
RL   J. Mol. Biol. 253:100-113(1995).
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   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000250};
CC   -!- SUBUNIT: Homodimer.
CC   -!- INTERACTION:
CC       P0A8N3; P0AAM3: hypC; NbExp=3; IntAct=EBI-552719, EBI-552654;
CC       P0A8N3; P43672: uup; NbExp=2; IntAct=EBI-552719, EBI-559429;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm.
CC   -!- MISCELLANEOUS: There are two lysyl-tRNA ligases in E.coli: lysS is
CC       expressed constitutively, while lysU is heat inducible.
CC   -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC       {ECO:0000305}.
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DR   EMBL; J03795; AAA23959.1; -; Genomic_DNA.
DR   EMBL; U28375; AAA83071.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC75928.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE76955.1; -; Genomic_DNA.
DR   PIR; B65073; SYECKT.
DR   RefSeq; NP_417366.1; NC_000913.3.
DR   RefSeq; WP_000003071.1; NZ_SSZK01000003.1.
DR   PDB; 1BBU; X-ray; 2.70 A; A=2-505.
DR   PDB; 1BBW; X-ray; 2.70 A; A=2-505.
DR   PDB; 1KRS; NMR; -; A=31-149.
DR   PDB; 1KRT; NMR; -; A=31-149.
DR   PDBsum; 1BBU; -.
DR   PDBsum; 1BBW; -.
DR   PDBsum; 1KRS; -.
DR   PDBsum; 1KRT; -.
DR   AlphaFoldDB; P0A8N3; -.
DR   BMRB; P0A8N3; -.
DR   SMR; P0A8N3; -.
DR   BioGRID; 4262337; 591.
DR   DIP; DIP-36211N; -.
DR   IntAct; P0A8N3; 25.
DR   STRING; 511145.b2890; -.
DR   jPOST; P0A8N3; -.
DR   PaxDb; 511145-b2890; -.
DR   EnsemblBacteria; AAC75928; AAC75928; b2890.
DR   GeneID; 947372; -.
DR   KEGG; ecj:JW2858; -.
DR   KEGG; eco:b2890; -.
DR   PATRIC; fig|1411691.4.peg.3844; -.
DR   EchoBASE; EB0547; -.
DR   eggNOG; COG1190; Bacteria.
DR   HOGENOM; CLU_008255_6_0_6; -.
DR   InParanoid; P0A8N3; -.
DR   OMA; DFRNEGM; -.
DR   OrthoDB; 9801152at2; -.
DR   PhylomeDB; P0A8N3; -.
DR   BioCyc; EcoCyc:LYSS-MONOMER; -.
DR   BioCyc; MetaCyc:LYSS-MONOMER; -.
DR   BRENDA; 6.1.1.6; 2026.
DR   EvolutionaryTrace; P0A8N3; -.
DR   PRO; PR:P0A8N3; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0016874; F:ligase activity; IDA:EcoliWiki.
DR   GO; GO:0004824; F:lysine-tRNA ligase activity; IDA:EcoCyc.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR   GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR   GO; GO:0006430; P:lysyl-tRNA aminoacylation; IGI:EcoliWiki.
DR   GO; GO:0006418; P:tRNA aminoacylation for protein translation; IGI:EcoliWiki.
DR   CDD; cd00775; LysRS_core; 1.
DR   CDD; cd04322; LysRS_N; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 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   NCBIfam; TIGR00499; lysS_bact; 1.
DR   PANTHER; PTHR42918:SF9; LYSINE--TRNA LIGASE; 1.
DR   PANTHER; PTHR42918; LYSYL-TRNA SYNTHETASE; 1.
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; SSF55681; Class II aaRS and biotin synthetases; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
DR   SWISS-2DPAGE; P0A8N3; -.
PE   1: Evidence at protein level;
KW   3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW   Direct protein sequencing; Ligase; Magnesium; Metal-binding;
KW   Nucleotide-binding; Protein biosynthesis; Reference proteome.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000269|PubMed:2183178"
FT   CHAIN           2..505
FT                   /note="Lysine--tRNA ligase"
FT                   /id="PRO_0000152622"
FT   BINDING         415
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         422
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         422
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   HELIX           14..32
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           46..53
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           58..64
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          67..79
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          81..90
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          93..100
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   TURN            101..103
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           108..111
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           113..115
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          118..120
FT                   /evidence="ECO:0007829|PDB:1KRS"
FT   STRAND          121..130
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          131..135
FT                   /evidence="ECO:0007829|PDB:1KRS"
FT   STRAND          136..147
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           165..168
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           170..176
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           178..199
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   TURN            200..202
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          210..214
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          224..227
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   TURN            228..231
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          232..236
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           241..249
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          254..262
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          273..284
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           287..306
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          309..313
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          316..322
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          325..328
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           329..336
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           342..346
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           348..357
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           368..380
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           381..383
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          386..394
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           395..397
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          399..401
FT                   /evidence="ECO:0007829|PDB:1BBW"
FT   STRAND          410..418
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          421..429
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           433..448
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           459..466
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          471..478
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           479..487
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   HELIX           492..494
FT                   /evidence="ECO:0007829|PDB:1BBU"
FT   STRAND          496..498
FT                   /evidence="ECO:0007829|PDB:1BBW"
SQ   SEQUENCE   505 AA;  57603 MW;  F2CA901FBA63CFEF CRC64;
     MSEQHAQGAD AVVDLNNELK TRREKLANLR EQGIAFPNDF RRDHTSDQLH AEFDGKENEE
     LEALNIEVAV AGRMMTRRIM GKASFVTLQD VGGRIQLYVA RDDLPEGVYN EQFKKWDLGD
     ILGAKGKLFK TKTGELSIHC TELRLLTKAL RPLPDKFHGL QDQEARYRQR YLDLISNDES
     RNTFKVRSQI LSGIRQFMVN RGFMEVETPM MQVIPGGAAA RPFITHHNAL DLDMYLRIAP
     ELYLKRLVVG GFERVFEINR NFRNEGISVR HNPEFTMMEL YMAYADYKDL IELTESLFRT
     LAQDILGKTE VTYGDVTLDF GKPFEKLTMR EAIKKYRPET DMADLDNFDS AKAIAESIGI
     HVEKSWGLGR IVTEIFEEVA EAHLIQPTFI TEYPAEVSPL ARRNDVNPEI TDRFEFFIGG
     REIGNGFSEL NDAEDQAQRF LDQVAAKDAG DDEAMFYDED YVTALEHGLP PTAGLGIGID
     RMVMLFTNSH TIRDVILFPA MRPVK
//