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P0A8N3

- SYK1_ECOLI

UniProt

P0A8N3 - SYK1_ECOLI

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Protein

Lysine--tRNA ligase

Gene

lysS

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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

Binds 3 magnesium 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

  1. ATP binding Source: UniProtKB-HAMAP
  2. ligase activity Source: EcoliWiki
  3. lysine-tRNA ligase activity Source: EcoliWiki
  4. magnesium ion binding Source: UniProtKB-HAMAP
  5. nucleic acid binding Source: InterPro

GO - Biological processi

  1. lysyl-tRNA aminoacylation Source: EcoliWiki
  2. 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.

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: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10552. lysS.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: UniProtKB
  2. 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.

PTM databases

PhosSiteiP0809407.

Expressioni

Gene expression databases

GenevestigatoriP0A8N3.

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.
OMAiGTEICLE.
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]
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:
EMBL
GenBank
DDBJ
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.
YP_491091.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75928; AAC75928; b2890.
BAE76955; BAE76955; BAE76955.
GeneIDi12933343.
947372.
KEGGiecj:Y75_p2822.
eco:b2890.
PATRICi32121190. VBIEscCol129921_2983.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
PIRi B65073. SYECKT.
RefSeqi NP_417366.1. NC_000913.3.
YP_491091.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1BBU X-ray 2.70 A 2-505 [» ]
1BBW X-ray 2.70 A 2-505 [» ]
1KRS NMR - A 31-149 [» ]
1KRT NMR - A 31-149 [» ]
ProteinModelPortali P0A8N3.
SMRi P0A8N3. Positions 12-503.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-36211N.
IntActi P0A8N3. 24 interactions.
MINTi MINT-1227180.
STRINGi 511145.b2890.

PTM databases

PhosSitei P0809407.

2D gel databases

SWISS-2DPAGE P0A8N3.

Proteomic databases

PaxDbi P0A8N3.
PRIDEi P0A8N3.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75928 ; AAC75928 ; b2890 .
BAE76955 ; BAE76955 ; BAE76955 .
GeneIDi 12933343.
947372.
KEGGi ecj:Y75_p2822.
eco:b2890.
PATRICi 32121190. VBIEscCol129921_2983.

Organism-specific databases

EchoBASEi EB0547.
EcoGenei EG10552. lysS.

Phylogenomic databases

eggNOGi COG1190.
HOGENOMi HOG000236578.
InParanoidi P0A8N3.
KOi K04567.
OMAi GTEICLE.
OrthoDBi EOG69PQ2M.
PhylomeDBi P0A8N3.

Enzyme and pathway databases

BioCyci EcoCyc:LYSS-MONOMER.
ECOL316407:JW2858-MONOMER.
MetaCyc:LYSS-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0A8N3.
PROi P0A8N3.

Gene expression databases

Genevestigatori P0A8N3.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
HAMAPi MF_00252. Lys_tRNA_synth_class2.
InterProi IPR004364. 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 ]
PANTHERi PTHR22594. PTHR22594. 1 hit.
Pfami PF00152. tRNA-synt_2. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view ]
PRINTSi PR00982. TRNASYNTHLYS.
SUPFAMi SSF50249. SSF50249. 1 hit.
TIGRFAMsi TIGR00499. lysS_bact. 1 hit.
PROSITEi PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: October 29, 2014
This is version 97 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