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Protein

Lysine--tRNA ligase

Gene

lysS

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).

Cofactori

Mg2+By similarityNote: Binds 3 Mg2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi415 – 4151Magnesium 1By similarity
Metal bindingi422 – 4221Magnesium 1By similarity
Metal bindingi422 – 4221Magnesium 2By similarity

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • ligase activity Source: EcoliWiki
  • lysine-tRNA ligase activity Source: EcoliWiki
  • magnesium ion binding Source: UniProtKB-HAMAP
  • nucleic acid binding Source: InterPro

GO - Biological processi

  • lysyl-tRNA aminoacylation Source: EcoliWiki
  • tRNA aminoacylation for protein translation Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Aminoacyl-tRNA synthetase, Ligase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:LYSS-MONOMER.
ECOL316407:JW2858-MONOMER.
MetaCyc:LYSS-MONOMER.
BRENDAi6.1.1.6. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine--tRNA ligase (EC:6.1.1.6)
Alternative name(s):
Lysyl-tRNA synthetase
Short name:
LysRS
Gene namesi
Name:lysS
Synonyms:asuD, herC
Ordered Locus Names:b2890, JW2858
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10552. lysS.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 505504Lysine--tRNA ligasePRO_0000152622Add
BLAST

Proteomic databases

PaxDbiP0A8N3.
PRIDEiP0A8N3.

2D gel databases

SWISS-2DPAGEP0A8N3.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

DIPiDIP-36211N.
IntActiP0A8N3. 24 interactions.
MINTiMINT-1227180.
STRINGi511145.b2890.

Structurei

Secondary structure

1
505
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi14 – 3219Combined sources
Helixi46 – 538Combined sources
Helixi58 – 647Combined sources
Beta strandi67 – 7913Combined sources
Beta strandi81 – 9010Combined sources
Beta strandi93 – 1008Combined sources
Turni101 – 1033Combined sources
Helixi108 – 1114Combined sources
Helixi113 – 1153Combined sources
Beta strandi118 – 1203Combined sources
Beta strandi121 – 13010Combined sources
Beta strandi131 – 1355Combined sources
Beta strandi136 – 14712Combined sources
Helixi165 – 1684Combined sources
Helixi170 – 1767Combined sources
Helixi178 – 19922Combined sources
Turni200 – 2023Combined sources
Beta strandi210 – 2145Combined sources
Beta strandi224 – 2274Combined sources
Turni228 – 2314Combined sources
Beta strandi232 – 2365Combined sources
Helixi241 – 2499Combined sources
Beta strandi254 – 2629Combined sources
Beta strandi273 – 28412Combined sources
Helixi287 – 30620Combined sources
Beta strandi309 – 3135Combined sources
Beta strandi316 – 3227Combined sources
Beta strandi325 – 3284Combined sources
Helixi329 – 3368Combined sources
Helixi342 – 3465Combined sources
Helixi348 – 35710Combined sources
Helixi368 – 38013Combined sources
Helixi381 – 3833Combined sources
Beta strandi386 – 3949Combined sources
Helixi395 – 3973Combined sources
Beta strandi399 – 4013Combined sources
Beta strandi410 – 4189Combined sources
Beta strandi421 – 4299Combined sources
Helixi433 – 44816Combined sources
Helixi459 – 4668Combined sources
Beta strandi471 – 4788Combined sources
Helixi479 – 4879Combined sources
Helixi492 – 4943Combined sources
Beta strandi496 – 4983Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BBUX-ray2.70A2-505[»]
1BBWX-ray2.70A2-505[»]
1KRSNMR-A31-149[»]
1KRTNMR-A31-149[»]
ProteinModelPortaliP0A8N3.
SMRiP0A8N3. Positions 12-503.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8N3.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1190.
HOGENOMiHOG000236578.
InParanoidiP0A8N3.
KOiK04567.
OMAiCGDQLFE.
OrthoDBiEOG69PQ2M.
PhylomeDBiP0A8N3.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_00252. Lys_tRNA_synth_class2.
InterProiIPR004364. aa-tRNA-synt_II.
IPR018150. aa-tRNA-synt_II-like.
IPR006195. aa-tRNA-synth_II.
IPR002313. Lys-tRNA-ligase_II.
IPR018149. Lys-tRNA-synth_II_C.
IPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA.
[Graphical view]
PANTHERiPTHR22594. PTHR22594. 1 hit.
PfamiPF00152. tRNA-synt_2. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view]
PIRSFiPIRSF039101. LysRS2. 1 hit.
PRINTSiPR00982. TRNASYNTHLYS.
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00499. lysS_bact. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A8N3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEQHAQGAD AVVDLNNELK TRREKLANLR EQGIAFPNDF RRDHTSDQLH
60 70 80 90 100
AEFDGKENEE LEALNIEVAV AGRMMTRRIM GKASFVTLQD VGGRIQLYVA
110 120 130 140 150
RDDLPEGVYN EQFKKWDLGD ILGAKGKLFK TKTGELSIHC TELRLLTKAL
160 170 180 190 200
RPLPDKFHGL QDQEARYRQR YLDLISNDES RNTFKVRSQI LSGIRQFMVN
210 220 230 240 250
RGFMEVETPM MQVIPGGAAA RPFITHHNAL DLDMYLRIAP ELYLKRLVVG
260 270 280 290 300
GFERVFEINR NFRNEGISVR HNPEFTMMEL YMAYADYKDL IELTESLFRT
310 320 330 340 350
LAQDILGKTE VTYGDVTLDF GKPFEKLTMR EAIKKYRPET DMADLDNFDS
360 370 380 390 400
AKAIAESIGI HVEKSWGLGR IVTEIFEEVA EAHLIQPTFI TEYPAEVSPL
410 420 430 440 450
ARRNDVNPEI TDRFEFFIGG REIGNGFSEL NDAEDQAQRF LDQVAAKDAG
460 470 480 490 500
DDEAMFYDED YVTALEHGLP PTAGLGIGID RMVMLFTNSH TIRDVILFPA

MRPVK
Length:505
Mass (Da):57,603
Last modified:January 23, 2007 - v2
Checksum:iF2CA901FBA63CFEF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03795 Genomic DNA. Translation: AAA23959.1.
U28375 Genomic DNA. Translation: AAA83071.1.
U00096 Genomic DNA. Translation: AAC75928.1.
AP009048 Genomic DNA. Translation: BAE76955.1.
PIRiB65073. SYECKT.
RefSeqiNP_417366.1. NC_000913.3.
WP_000003071.1. NZ_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC75928; AAC75928; b2890.
BAE76955; BAE76955; BAE76955.
GeneIDi947372.
KEGGieco:b2890.
PATRICi32121190. VBIEscCol129921_2983.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03795 Genomic DNA. Translation: AAA23959.1.
U28375 Genomic DNA. Translation: AAA83071.1.
U00096 Genomic DNA. Translation: AAC75928.1.
AP009048 Genomic DNA. Translation: BAE76955.1.
PIRiB65073. SYECKT.
RefSeqiNP_417366.1. NC_000913.3.
WP_000003071.1. NZ_CP010445.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BBUX-ray2.70A2-505[»]
1BBWX-ray2.70A2-505[»]
1KRSNMR-A31-149[»]
1KRTNMR-A31-149[»]
ProteinModelPortaliP0A8N3.
SMRiP0A8N3. Positions 12-503.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-36211N.
IntActiP0A8N3. 24 interactions.
MINTiMINT-1227180.
STRINGi511145.b2890.

2D gel databases

SWISS-2DPAGEP0A8N3.

Proteomic databases

PaxDbiP0A8N3.
PRIDEiP0A8N3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75928; AAC75928; b2890.
BAE76955; BAE76955; BAE76955.
GeneIDi947372.
KEGGieco:b2890.
PATRICi32121190. VBIEscCol129921_2983.

Organism-specific databases

EchoBASEiEB0547.
EcoGeneiEG10552. lysS.

Phylogenomic databases

eggNOGiCOG1190.
HOGENOMiHOG000236578.
InParanoidiP0A8N3.
KOiK04567.
OMAiCGDQLFE.
OrthoDBiEOG69PQ2M.
PhylomeDBiP0A8N3.

Enzyme and pathway databases

BioCyciEcoCyc:LYSS-MONOMER.
ECOL316407:JW2858-MONOMER.
MetaCyc:LYSS-MONOMER.
BRENDAi6.1.1.6. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A8N3.
PROiP0A8N3.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_00252. Lys_tRNA_synth_class2.
InterProiIPR004364. aa-tRNA-synt_II.
IPR018150. aa-tRNA-synt_II-like.
IPR006195. aa-tRNA-synth_II.
IPR002313. Lys-tRNA-ligase_II.
IPR018149. Lys-tRNA-synth_II_C.
IPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA.
[Graphical view]
PANTHERiPTHR22594. PTHR22594. 1 hit.
PfamiPF00152. tRNA-synt_2. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view]
PIRSFiPIRSF039101. LysRS2. 1 hit.
PRINTSiPR00982. TRNASYNTHLYS.
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00499. lysS_bact. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Chromosomal location and structure of the operon encoding peptide-chain-release factor 2 of Escherichia coli."
    Kawakami K., Joensson Y.H., Bjoerk G.R., Ikeda H., Nakamura Y.
    Proc. Natl. Acad. Sci. U.S.A. 85:5620-5624(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Homology of lysS and lysU, the two Escherichia coli genes encoding distinct lysyl-tRNA synthetase species."
    Leveque F., Plateau P., Dessen P., Blanquet S.
    Nucleic Acids Res. 18:305-312(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-28.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  6. "Solution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys)."
    Commans S., Plateau P., Blanquet S., Dardel F.
    J. Mol. Biol. 253:100-113(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.

Entry informationi

Entry nameiSYK1_ECOLI
AccessioniPrimary (citable) accession number: P0A8N3
Secondary accession number(s): P13030, Q2M9V1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: July 22, 2015
This is version 105 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

There are two lysyl-tRNA ligases in E.coli: lysS is expressed constitutively, while lysU is heat inducible.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.