Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
Metal bindingi415Magnesium 1By similarity1
Metal bindingi422Magnesium 1By similarity1
Metal bindingi422Magnesium 2By similarity1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001526222 – 505Lysine--tRNA ligaseAdd BLAST504

Proteomic databases

EPDiP0A8N3.
PaxDbiP0A8N3.
PRIDEiP0A8N3.

2D gel databases

SWISS-2DPAGEP0A8N3.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi4262337. 587 interactors.
DIPiDIP-36211N.
IntActiP0A8N3. 24 interactors.
MINTiMINT-1227180.
STRINGi511145.b2890.

Structurei

Secondary structure

1505
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 32Combined sources19
Helixi46 – 53Combined sources8
Helixi58 – 64Combined sources7
Beta strandi67 – 79Combined sources13
Beta strandi81 – 90Combined sources10
Beta strandi93 – 100Combined sources8
Turni101 – 103Combined sources3
Helixi108 – 111Combined sources4
Helixi113 – 115Combined sources3
Beta strandi118 – 120Combined sources3
Beta strandi121 – 130Combined sources10
Beta strandi131 – 135Combined sources5
Beta strandi136 – 147Combined sources12
Helixi165 – 168Combined sources4
Helixi170 – 176Combined sources7
Helixi178 – 199Combined sources22
Turni200 – 202Combined sources3
Beta strandi210 – 214Combined sources5
Beta strandi224 – 227Combined sources4
Turni228 – 231Combined sources4
Beta strandi232 – 236Combined sources5
Helixi241 – 249Combined sources9
Beta strandi254 – 262Combined sources9
Beta strandi273 – 284Combined sources12
Helixi287 – 306Combined sources20
Beta strandi309 – 313Combined sources5
Beta strandi316 – 322Combined sources7
Beta strandi325 – 328Combined sources4
Helixi329 – 336Combined sources8
Helixi342 – 346Combined sources5
Helixi348 – 357Combined sources10
Helixi368 – 380Combined sources13
Helixi381 – 383Combined sources3
Beta strandi386 – 394Combined sources9
Helixi395 – 397Combined sources3
Beta strandi399 – 401Combined sources3
Beta strandi410 – 418Combined sources9
Beta strandi421 – 429Combined sources9
Helixi433 – 448Combined sources16
Helixi459 – 466Combined sources8
Beta strandi471 – 478Combined sources8
Helixi479 – 487Combined sources9
Helixi492 – 494Combined sources3
Beta strandi496 – 498Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP0A8N3.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CRK. Bacteria.
COG1190. LUCA.
HOGENOMiHOG000236578.
InParanoidiP0A8N3.
KOiK04567.
OMAiRYELYIG.
PhylomeDBiP0A8N3.

Family and domain databases

CDDicd00775. LysRS_core. 1 hit.
HAMAPiMF_00252. Lys_tRNA_synth_class2. 1 hit.
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_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75928; AAC75928; b2890.
BAE76955; BAE76955; BAE76955.
GeneIDi947372.
KEGGiecj:JW2858.
eco: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_LN832404.1.

3D structure databases

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

Protein-protein interaction databases

BioGridi4262337. 587 interactors.
DIPiDIP-36211N.
IntActiP0A8N3. 24 interactors.
MINTiMINT-1227180.
STRINGi511145.b2890.

2D gel databases

SWISS-2DPAGEP0A8N3.

Proteomic databases

EPDiP0A8N3.
PaxDbiP0A8N3.
PRIDEiP0A8N3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75928; AAC75928; b2890.
BAE76955; BAE76955; BAE76955.
GeneIDi947372.
KEGGiecj:JW2858.
eco:b2890.
PATRICi32121190. VBIEscCol129921_2983.

Organism-specific databases

EchoBASEiEB0547.
EcoGeneiEG10552. lysS.

Phylogenomic databases

eggNOGiENOG4105CRK. Bacteria.
COG1190. LUCA.
HOGENOMiHOG000236578.
InParanoidiP0A8N3.
KOiK04567.
OMAiRYELYIG.
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

CDDicd00775. LysRS_core. 1 hit.
HAMAPiMF_00252. Lys_tRNA_synth_class2. 1 hit.
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...

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: November 2, 2016
This is version 113 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

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 one 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.