SYK2_ECOLI
ID SYK2_ECOLI Reviewed; 505 AA.
AC P0A8N5; P14825; Q2M6H4;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Lysine--tRNA ligase, heat inducible;
DE EC=6.1.1.6;
DE AltName: Full=Lysyl-tRNA synthetase;
DE Short=LysRS;
GN Name=lysU; OrderedLocusNames=b4129, JW4090;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-21.
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 [2]
RP SEQUENCE REVISION TO 446.
RA Dessen P.;
RL Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2188953; DOI=10.1128/jb.172.6.3237-3243.1990;
RA Clark R.L., Neidhardt F.C.;
RT "Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of
RT nucleotide sequences and mutant behavior.";
RL J. Bacteriol. 172:3237-3243(1990).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [5]
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 [6]
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 [7]
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 [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-114 AND LYS-156, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX PubMed=18723842; DOI=10.1074/mcp.m800187-mcp200;
RA Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA Grishin N.V., Zhao Y.;
RT "Lysine acetylation is a highly abundant and evolutionarily conserved
RT modification in Escherichia coli.";
RL Mol. Cell. Proteomics 8:215-225(2009).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
RX PubMed=7735833; DOI=10.1016/s0969-2126(01)00147-2;
RA Onesti S., Miller A.D., Brick P.;
RT "The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia
RT coli.";
RL Structure 3:163-176(1995).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.12 ANGSTROMS).
RX PubMed=10913247; DOI=10.1021/bi0006722;
RA Desogus G., Todone F., Brick P., Onesti S.;
RT "Active site of lysyl-tRNA synthetase: structural studies of the
RT adenylation reaction.";
RL Biochemistry 39:8418-8425(2000).
CC -!- FUNCTION: Can also synthesize a number of adenyl dinucleotides (in
CC particular AppppA). These dinucleotides have been proposed to act as
CC modulators of the heat-shock response and stress response.
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;
CC Note=Binds 3 Mg(2+) ions per subunit. The third one is coordinated by
CC ATP.;
CC -!- SUBUNIT: Homodimer.
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; X16542; CAA34542.1; -; Genomic_DNA.
DR EMBL; M30630; AAA24096.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97029.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77090.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78132.1; -; Genomic_DNA.
DR PIR; S56358; SYECKU.
DR RefSeq; NP_418553.1; NC_000913.3.
DR RefSeq; WP_001295074.1; NZ_STEB01000014.1.
DR PDB; 1E1O; X-ray; 2.12 A; A=2-505.
DR PDB; 1E1T; X-ray; 2.40 A; A=2-505.
DR PDB; 1E22; X-ray; 2.43 A; A=2-505.
DR PDB; 1E24; X-ray; 2.35 A; A=2-505.
DR PDB; 1LYL; X-ray; 2.80 A; A/B/C=2-505.
DR PDB; 5YZX; X-ray; 3.20 A; A/B/C=1-505.
DR PDBsum; 1E1O; -.
DR PDBsum; 1E1T; -.
DR PDBsum; 1E22; -.
DR PDBsum; 1E24; -.
DR PDBsum; 1LYL; -.
DR PDBsum; 5YZX; -.
DR AlphaFoldDB; P0A8N5; -.
DR SMR; P0A8N5; -.
DR BioGRID; 4262688; 18.
DR DIP; DIP-36212N; -.
DR IntAct; P0A8N5; 52.
DR STRING; 511145.b4129; -.
DR iPTMnet; P0A8N5; -.
DR jPOST; P0A8N5; -.
DR PaxDb; P0A8N5; -.
DR PRIDE; P0A8N5; -.
DR EnsemblBacteria; AAC77090; AAC77090; b4129.
DR EnsemblBacteria; BAE78132; BAE78132; BAE78132.
DR GeneID; 66671959; -.
DR GeneID; 948645; -.
DR KEGG; ecj:JW4090; -.
DR KEGG; eco:b4129; -.
DR PATRIC; fig|1411691.4.peg.2570; -.
DR EchoBASE; EB0548; -.
DR eggNOG; COG1190; Bacteria.
DR HOGENOM; CLU_008255_6_0_6; -.
DR InParanoid; P0A8N5; -.
DR OMA; GRFENQI; -.
DR PhylomeDB; P0A8N5; -.
DR BioCyc; EcoCyc:LYSU-MON; -.
DR BioCyc; MetaCyc:LYSU-MON; -.
DR BRENDA; 6.1.1.6; 2026.
DR EvolutionaryTrace; P0A8N5; -.
DR PRO; PR:P0A8N5; -.
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; IDA:EcoliWiki.
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; IDA:EcoliWiki.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IDA:EcoCyc.
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; Acetylation; Aminoacyl-tRNA synthetase; ATP-binding;
KW Cytoplasm; 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, heat inducible"
FT /id="PRO_0000152627"
FT BINDING 415
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 422
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 422
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT MOD_RES 114
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT MOD_RES 156
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT CONFLICT 125
FT /note="Missing (in Ref. 3; AAA24096)"
FT /evidence="ECO:0000305"
FT CONFLICT 236
FT /note="L -> A (in Ref. 3; AAA24096)"
FT /evidence="ECO:0000305"
FT CONFLICT 258..262
FT /note="INRNF -> HVT (in Ref. 3; AAA24096)"
FT /evidence="ECO:0000305"
FT CONFLICT 268..269
FT /note="SV -> R (in Ref. 3; AAA24096)"
FT /evidence="ECO:0000305"
FT CONFLICT 351
FT /note="A -> R (in Ref. 3; AAA24096)"
FT /evidence="ECO:0000305"
FT CONFLICT 371
FT /note="I -> S (in Ref. 3; AAA24096)"
FT /evidence="ECO:0000305"
FT CONFLICT 380..384
FT /note="AEAHL -> VEGHV (in Ref. 3; AAA24096)"
FT /evidence="ECO:0000305"
FT CONFLICT 388
FT /note="T -> S (in Ref. 3; AAA24096)"
FT /evidence="ECO:0000305"
FT HELIX 13..32
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 46..53
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 58..64
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 67..80
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 83..90
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 93..100
FT /evidence="ECO:0007829|PDB:1E1O"
FT TURN 101..103
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 108..111
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 121..130
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 136..147
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 165..168
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 170..176
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 178..199
FT /evidence="ECO:0007829|PDB:1E1O"
FT TURN 200..202
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 210..214
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 224..227
FT /evidence="ECO:0007829|PDB:1E1O"
FT TURN 228..231
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 232..236
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 241..250
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 254..262
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 273..284
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 287..306
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 307..313
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 316..319
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 325..328
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 329..336
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 342..346
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 348..357
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 368..379
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 381..383
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 388..391
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 395..397
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 410..418
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 421..429
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 433..448
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 459..468
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 471..478
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 479..486
FT /evidence="ECO:0007829|PDB:1E1O"
FT HELIX 492..494
FT /evidence="ECO:0007829|PDB:1E1O"
FT STRAND 496..498
FT /evidence="ECO:0007829|PDB:1E1O"
SQ SEQUENCE 505 AA; 57827 MW; 547415F5875396E0 CRC64;
MSEQETRGAN EAIDFNDELR NRREKLAALR QQGVAFPNDF RRDHTSDQLH EEFDAKDNQE
LESLNIEVSV AGRMMTRRIM GKASFVTLQD VGGRIQLYVA RDSLPEGVYN DQFKKWDLGD
IIGARGTLFK TQTGELSIHC TELRLLTKAL RPLPDKFHGL QDQEVRYRQR YLDLIANDKS
RQTFVVRSKI LAAIRQFMVA RGFMEVETPM MQVIPGGASA RPFITHHNAL DLDMYLRIAP
ELYLKRLVVG GFERVFEINR NFRNEGISVR HNPEFTMMEL YMAYADYHDL IELTESLFRT
LAQEVLGTTK VTYGEHVFDF GKPFEKLTMR EAIKKYRPET DMADLDNFDA AKALAESIGI
TVEKSWGLGR IVTEIFDEVA EAHLIQPTFI TEYPAEVSPL ARRNDVNPEI TDRFEFFIGG
REIGNGFSEL NDAEDQAERF QEQVNAKAAG DDEAMFYDED YVTALEYGLP PTAGLGIGID
RMIMLFTNSH TIRDVILFPA MRPQK
