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Protein

Lysine--tRNA ligase, heat inducible

Gene

lysU

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

Functioni

Also can synthesize a number of adenyl dinucleotides (in particular AppppA). These dinucleotides have been proposed to act as modulators of the heat-shock response and stress response.

Catalytic activityi

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

Cofactori

Mg2+Note: Binds 3 Mg2+ ions per subunit. The third one is coordinated by ATP.

Sites

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

GO - Molecular functioni

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

GO - Biological processi

  • lysyl-tRNA aminoacylation Source: EcoCyc
  • 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:LYSU-MONOMER.
ECOL316407:JW4090-MONOMER.
MetaCyc:LYSU-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine--tRNA ligase, heat inducible (EC:6.1.1.6)
Alternative name(s):
Lysyl-tRNA synthetase
Short name:
LysRS
Gene namesi
Name:lysU
Ordered Locus Names:b4129, JW4090
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10553. lysU.

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 methionineiRemoved1 Publication
Chaini2 – 505504Lysine--tRNA ligase, heat induciblePRO_0000152627Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei114 – 1141N6-acetyllysine1 Publication
Modified residuei156 – 1561N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP0A8N5.
PaxDbiP0A8N5.
PRIDEiP0A8N5.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi4262688. 6 interactions.
DIPiDIP-36212N.
IntActiP0A8N5. 51 interactions.
MINTiMINT-1219496.
STRINGi511145.b4129.

Structurei

Secondary structure

1
505
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 3220Combined sources
Helixi46 – 538Combined sources
Helixi58 – 647Combined sources
Beta strandi67 – 8014Combined sources
Beta strandi83 – 908Combined sources
Beta strandi93 – 1008Combined sources
Turni101 – 1033Combined sources
Helixi108 – 1114Combined sources
Helixi113 – 1153Combined sources
Beta strandi121 – 13010Combined 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 – 25010Combined sources
Beta strandi254 – 2629Combined sources
Beta strandi273 – 28412Combined sources
Helixi287 – 30620Combined sources
Beta strandi307 – 3137Combined sources
Beta strandi316 – 3194Combined sources
Beta strandi325 – 3284Combined sources
Helixi329 – 3368Combined sources
Helixi342 – 3465Combined sources
Helixi348 – 35710Combined sources
Helixi368 – 37912Combined sources
Helixi381 – 3833Combined sources
Beta strandi388 – 3914Combined sources
Helixi395 – 3973Combined sources
Beta strandi410 – 4189Combined sources
Beta strandi421 – 4299Combined sources
Helixi433 – 44816Combined sources
Helixi459 – 46810Combined sources
Beta strandi471 – 4788Combined sources
Helixi479 – 4868Combined sources
Helixi492 – 4943Combined sources
Beta strandi496 – 4983Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1E1OX-ray2.12A2-505[»]
1E1TX-ray2.40A2-505[»]
1E22X-ray2.43A2-505[»]
1E24X-ray2.35A2-505[»]
1LYLX-ray2.80A/B/C2-505[»]
ProteinModelPortaliP0A8N5.
SMRiP0A8N5. Positions 12-503.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8N5.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CRK. Bacteria.
COG1190. LUCA.
HOGENOMiHOG000236578.
InParanoidiP0A8N5.
KOiK04567.
OMAiTTFHTQS.
OrthoDBiEOG69PQ2M.
PhylomeDBiP0A8N5.

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.

P0A8N5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEQETRGAN EAIDFNDELR NRREKLAALR QQGVAFPNDF RRDHTSDQLH
60 70 80 90 100
EEFDAKDNQE LESLNIEVSV AGRMMTRRIM GKASFVTLQD VGGRIQLYVA
110 120 130 140 150
RDSLPEGVYN DQFKKWDLGD IIGARGTLFK TQTGELSIHC TELRLLTKAL
160 170 180 190 200
RPLPDKFHGL QDQEVRYRQR YLDLIANDKS RQTFVVRSKI LAAIRQFMVA
210 220 230 240 250
RGFMEVETPM MQVIPGGASA RPFITHHNAL DLDMYLRIAP ELYLKRLVVG
260 270 280 290 300
GFERVFEINR NFRNEGISVR HNPEFTMMEL YMAYADYHDL IELTESLFRT
310 320 330 340 350
LAQEVLGTTK VTYGEHVFDF GKPFEKLTMR EAIKKYRPET DMADLDNFDA
360 370 380 390 400
AKALAESIGI TVEKSWGLGR IVTEIFDEVA EAHLIQPTFI TEYPAEVSPL
410 420 430 440 450
ARRNDVNPEI TDRFEFFIGG REIGNGFSEL NDAEDQAERF QEQVNAKAAG
460 470 480 490 500
DDEAMFYDED YVTALEYGLP PTAGLGIGID RMIMLFTNSH TIRDVILFPA

MRPQK
Length:505
Mass (Da):57,827
Last modified:January 23, 2007 - v2
Checksum:i547415F5875396E0
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti125 – 1251Missing in AAA24096 (PubMed:2188953).Curated
Sequence conflicti236 – 2361L → A in AAA24096 (PubMed:2188953).Curated
Sequence conflicti258 – 2625INRNF → HVT in AAA24096 (PubMed:2188953).Curated
Sequence conflicti268 – 2692SV → R in AAA24096 (PubMed:2188953).Curated
Sequence conflicti351 – 3511A → R in AAA24096 (PubMed:2188953).Curated
Sequence conflicti371 – 3711I → S in AAA24096 (PubMed:2188953).Curated
Sequence conflicti380 – 3845AEAHL → VEGHV in AAA24096 (PubMed:2188953).Curated
Sequence conflicti388 – 3881T → S in AAA24096 (PubMed:2188953).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X16542 Genomic DNA. Translation: CAA34542.1.
M30630 Genomic DNA. Translation: AAA24096.1.
U14003 Genomic DNA. Translation: AAA97029.1.
U00096 Genomic DNA. Translation: AAC77090.1.
AP009048 Genomic DNA. Translation: BAE78132.1.
PIRiS56358. SYECKU.
RefSeqiNP_418553.1. NC_000913.3.
WP_001295074.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77090; AAC77090; b4129.
BAE78132; BAE78132; BAE78132.
GeneIDi948645.
KEGGiecj:JW4090.
eco:b4129.
PATRICi32123825. VBIEscCol129921_4261.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X16542 Genomic DNA. Translation: CAA34542.1.
M30630 Genomic DNA. Translation: AAA24096.1.
U14003 Genomic DNA. Translation: AAA97029.1.
U00096 Genomic DNA. Translation: AAC77090.1.
AP009048 Genomic DNA. Translation: BAE78132.1.
PIRiS56358. SYECKU.
RefSeqiNP_418553.1. NC_000913.3.
WP_001295074.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1E1OX-ray2.12A2-505[»]
1E1TX-ray2.40A2-505[»]
1E22X-ray2.43A2-505[»]
1E24X-ray2.35A2-505[»]
1LYLX-ray2.80A/B/C2-505[»]
ProteinModelPortaliP0A8N5.
SMRiP0A8N5. Positions 12-503.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262688. 6 interactions.
DIPiDIP-36212N.
IntActiP0A8N5. 51 interactions.
MINTiMINT-1219496.
STRINGi511145.b4129.

Proteomic databases

EPDiP0A8N5.
PaxDbiP0A8N5.
PRIDEiP0A8N5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77090; AAC77090; b4129.
BAE78132; BAE78132; BAE78132.
GeneIDi948645.
KEGGiecj:JW4090.
eco:b4129.
PATRICi32123825. VBIEscCol129921_4261.

Organism-specific databases

EchoBASEiEB0548.
EcoGeneiEG10553. lysU.

Phylogenomic databases

eggNOGiENOG4105CRK. Bacteria.
COG1190. LUCA.
HOGENOMiHOG000236578.
InParanoidiP0A8N5.
KOiK04567.
OMAiTTFHTQS.
OrthoDBiEOG69PQ2M.
PhylomeDBiP0A8N5.

Enzyme and pathway databases

BioCyciEcoCyc:LYSU-MONOMER.
ECOL316407:JW4090-MONOMER.
MetaCyc:LYSU-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A8N5.
PROiP0A8N5.

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. "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 2-21.
  2. Dessen P.
    Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 446.
  3. "Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of nucleotide sequences and mutant behavior."
    Clark R.L., Neidhardt F.C.
    J. Bacteriol. 172:3237-3243(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  6. "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.
  7. "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.
  8. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
    Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
    Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-114 AND LYS-156, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
  9. "The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli."
    Onesti S., Miller A.D., Brick P.
    Structure 3:163-176(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
  10. "Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction."
    Desogus G., Todone F., Brick P., Onesti S.
    Biochemistry 39:8418-8425(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.12 ANGSTROMS).

Entry informationi

Entry nameiSYK2_ECOLI
AccessioniPrimary (citable) accession number: P0A8N5
Secondary accession number(s): P14825, Q2M6H4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: March 16, 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.