SYK1_ECOLI
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 03-AUG-2022, entry version 146.
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; Proteobacteria; 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 SWISS-2DPAGE; P0A8N3; -.
DR jPOST; P0A8N3; -.
DR PaxDb; P0A8N3; -.
DR PRIDE; P0A8N3; -.
DR EnsemblBacteria; AAC75928; AAC75928; b2890.
DR EnsemblBacteria; BAE76955; BAE76955; BAE76955.
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; EIFGEKC; -.
DR PhylomeDB; P0A8N3; -.
DR BioCyc; EcoCyc:LYSS-MON; -.
DR BioCyc; MetaCyc:LYSS-MON; -.
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: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; -; 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 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
