Lysine--tRNA ligase - Escherichia coli (strain K12)

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P0A8N3 (SYK1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 85. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Lysine--tRNA ligase
EC=6.1.1.6

Alternative name(s):
Lysyl-tRNA synthetase
Short name=LysRS

Gene names

Name:	lysS
Synonyms:	asuD, herC
Ordered Locus Names:	b2890, JW2858

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	505 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys). HAMAP-Rule MF_00252
Cofactor	Binds 3 magnesium ions per subunit By similarity.
Subunit structure	Homodimer.
Subcellular location	Cytoplasm HAMAP-Rule MF_00252.
Miscellaneous	There are two lysyl-tRNA ligases in E.coli: lysS is expressed constitutively, while lysU is heat inducible. HAMAP-Rule MF_00252
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	lysyl-tRNA aminoacylation Inferred from genetic interaction PubMed 7782306. Source: EcoliWiki
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP lysine-tRNA ligase activity Inferred from genetic interaction PubMed 7782306. Source: EcoliWiki magnesium ion binding Inferred from electronic annotation. Source: HAMAP nucleic acid binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.2

Chain

2 – 505

504

Lysine--tRNA ligase HAMAP-Rule MF_00252

PRO_0000152622

Sites

Metal binding

415

Magnesium 1 By similarity

Metal binding

422

Magnesium 1 By similarity

Metal binding

422

Magnesium 2 By similarity

Secondary structure

505

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A8N3 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: F2CA901FBA63CFEF
Show »

FASTA

505

57,603

        10         20         30         40         50         60 
MSEQHAQGAD AVVDLNNELK TRREKLANLR EQGIAFPNDF RRDHTSDQLH AEFDGKENEE 

        70         80         90        100        110        120 
LEALNIEVAV AGRMMTRRIM GKASFVTLQD VGGRIQLYVA RDDLPEGVYN EQFKKWDLGD 

       130        140        150        160        170        180 
ILGAKGKLFK TKTGELSIHC TELRLLTKAL RPLPDKFHGL QDQEARYRQR YLDLISNDES 

       190        200        210        220        230        240 
RNTFKVRSQI LSGIRQFMVN RGFMEVETPM MQVIPGGAAA RPFITHHNAL DLDMYLRIAP 

       250        260        270        280        290        300 
ELYLKRLVVG GFERVFEINR NFRNEGISVR HNPEFTMMEL YMAYADYKDL IELTESLFRT 

       310        320        330        340        350        360 
LAQDILGKTE VTYGDVTLDF GKPFEKLTMR EAIKKYRPET DMADLDNFDS AKAIAESIGI 

       370        380        390        400        410        420 
HVEKSWGLGR IVTEIFEEVA EAHLIQPTFI TEYPAEVSPL ARRNDVNPEI TDRFEFFIGG 

       430        440        450        460        470        480 
REIGNGFSEL NDAEDQAQRF LDQVAAKDAG DDEAMFYDED YVTALEHGLP PTAGLGIGID 

       490        500 
RMVMLFTNSH TIRDVILFPA MRPVK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J03795 Genomic DNA. Translation: AAA23959.1.
U28375 Genomic DNA. Translation: AAA83071.1.
U00096 Genomic DNA. Translation: AAC75928.1.
AP009048 Genomic DNA. Translation: BAE76955.1.

PIR

SYECKT. B65073.

RefSeq

NP_417366.1. NC_000913.2.
YP_491091.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BBU	X-ray	2.70	A	2-504	[»]
1BBW	X-ray	2.70	A	2-504	[»]
1KRS	NMR	-	A	31-149	[»]
1KRT	NMR	-	A	31-149	[»]

ProteinModelPortal

P0A8N3.

SMR

P0A8N3. Positions 12-503.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36211N.

IntAct

P0A8N3. 24 interactions.

MINT

MINT-1227180.

STRING

511145.b2890.

PTM databases

PhosSite

P0809407.

2D gel databases

SWISS-2DPAGE

P0A8N3.

Proteomic databases

PaxDb

P0A8N3.

PRIDE

P0A8N3.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75928; AAC75928; b2890.
BAE76955; BAE76955; BAE76955.

GeneID

12933343.
947372.

KEGG

ecj:Y75_p2822.
eco:b2890.

PATRIC

32121190. VBIEscCol129921_2983.

Organism-specific databases

EchoBASE

EB0547.

EcoGene

EG10552. lysS.

Phylogenomic databases

eggNOG

COG1190.

HOGENOM

HOG000236578.

K04567.

OMA

FLEPECH.

ProtClustDB

PRK00484.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P0A8N3.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.

HAMAP

MF_00252. Lys_tRNA_synth_class2.

InterPro

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-helicase.
[Graphical view]

PANTHER

PTHR22594. PTHR22594. 1 hit.
PTHR22594:SF4. PTHR22594:SF4. 1 hit.

Pfam

PF00152. tRNA-synt_2. 1 hit.
PF01336. tRNA_anti. 1 hit.
[Graphical view]

PRINTS

PR00982. TRNASYNTHLYS.

SUPFAM

SSF50249. Nucleic_acid_OB. 1 hit.

TIGRFAMs

TIGR00499. lysS_bact. 1 hit.

PROSITE

PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A8N3.

Entry information

Entry name

SYK1_ECOLI

Accession

Primary (citable) accession number: P0A8N3
Secondary accession number(s): P13030, Q2M9V1

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 85 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents