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UniProtKB - P0A8N3 (SYK1_ECOLI)

Entry version 139 (07 Oct 2020)
Sequence version 2 (23 Jan 2007)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Miscellaneous

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi415Magnesium 1By similarity1
Metal bindingi422Magnesium 1By similarity1
Metal bindingi422Magnesium 2By similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionAminoacyl-tRNA synthetase, Ligase
Biological processProtein biosynthesis
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:LYSS-MONOMER
MetaCyc:LYSS-MONOMER

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		6.1.1.6, 2026

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Lysine--tRNA ligase (EC:6.1.1.6)
Alternative name(s):
Lysyl-tRNA synthetase
Short name:
LysRS
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:lysS
Synonyms:asuD, herC
Ordered Locus Names:b2890, JW2858
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Cytoplasm

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved1 Publication
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001526222 – 505Lysine--tRNA ligaseAdd BLAST504

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P0A8N3

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P0A8N3

PRoteomics IDEntifications database

More...PRIDEi		P0A8N3

2D gel databases

Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital

More...SWISS-2DPAGEi		P0A8N3

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Hide details

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4262337, 591 interactors

Database of interacting proteins

More...DIPi		DIP-36211N

Protein interaction database and analysis system

More...IntActi		P0A8N3, 25 interactors

STRING: functional protein association networks

More...STRINGi		511145.b2890

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1505
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Biological Magnetic Resonance Data Bank

More...BMRBi		P0A8N3

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P0A8N3

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P0A8N3

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the class-II aminoacyl-tRNA synthetase family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG1190, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_008255_6_0_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P0A8N3

KEGG Orthology (KO)

More...KOi		K04567

Database for complete collections of gene phylogenies

More...PhylomeDBi		P0A8N3

Family and domain databases

Conserved Domains Database

More...CDDi		cd00775, LysRS_core, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_00252, Lys_tRNA_synth_class2, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR004364, Aa-tRNA-synt_II
IPR006195, aa-tRNA-synth_II
IPR002313, Lys-tRNA-ligase_II
IPR034762, Lys-tRNA-ligase_II_bac/euk
IPR018149, Lys-tRNA-synth_II_C
IPR012340, NA-bd_OB-fold
IPR004365, NA-bd_OB_tRNA

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00152, tRNA-synt_2, 1 hit
PF01336, tRNA_anti-codon, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF039101, LysRS2, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00982, TRNASYNTHLYS

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF50249, SSF50249, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00499, lysS_bact, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50862, AA_TRNA_LIGASE_II, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iF2CA901FBA63CFEF
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...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

Protein sequence database of the Protein Information Resource

More...PIRi		B65073, SYECKT

NCBI Reference Sequences

More...RefSeqi		NP_417366.1, NC_000913.3
WP_000003071.1, NZ_SSZK01000003.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC75928; AAC75928; b2890
BAE76955; BAE76955; BAE76955

Database of genes from NCBI RefSeq genomes

More...GeneIDi		49583234
947372

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW2858
eco:b2890

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.3844

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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_SSZK01000003.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BBUX-ray2.70A2-505[»]
1BBWX-ray2.70A2-505[»]
1KRSNMR-A31-149[»]
1KRTNMR-A31-149[»]
BMRBiP0A8N3
SMRiP0A8N3
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4262337, 591 interactors
DIPiDIP-36211N
IntActiP0A8N3, 25 interactors
STRINGi511145.b2890

2D gel databases

SWISS-2DPAGEiP0A8N3

Proteomic databases

jPOSTiP0A8N3
PaxDbiP0A8N3
PRIDEiP0A8N3

Genome annotation databases

EnsemblBacteriaiAAC75928; AAC75928; b2890
BAE76955; BAE76955; BAE76955
GeneIDi49583234
947372
KEGGiecj:JW2858
eco:b2890
PATRICifig|1411691.4.peg.3844

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB0547

Phylogenomic databases

eggNOGiCOG1190, Bacteria
HOGENOMiCLU_008255_6_0_6
InParanoidiP0A8N3
KOiK04567
PhylomeDBiP0A8N3

Enzyme and pathway databases

BioCyciEcoCyc:LYSS-MONOMER
MetaCyc:LYSS-MONOMER
BRENDAi6.1.1.6, 2026

Miscellaneous databases

EvolutionaryTraceiP0A8N3

Protein Ontology

More...PROi		PR:P0A8N3

Family and domain databases

CDDicd00775, LysRS_core, 1 hit
HAMAPiMF_00252, Lys_tRNA_synth_class2, 1 hit
InterProiView protein in InterPro
IPR004364, Aa-tRNA-synt_II
IPR006195, aa-tRNA-synth_II
IPR002313, Lys-tRNA-ligase_II
IPR034762, Lys-tRNA-ligase_II_bac/euk
IPR018149, Lys-tRNA-synth_II_C
IPR012340, NA-bd_OB-fold
IPR004365, NA-bd_OB_tRNA
PfamiView protein in Pfam
PF00152, tRNA-synt_2, 1 hit
PF01336, tRNA_anti-codon, 1 hit
PIRSFiPIRSF039101, LysRS2, 1 hit
PRINTSiPR00982, TRNASYNTHLYS
SUPFAMiSSF50249, SSF50249, 1 hit
TIGRFAMsiTIGR00499, lysS_bact, 1 hit
PROSITEiView protein in PROSITE
PS50862, AA_TRNA_LIGASE_II, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiSYK1_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0A8N3
Secondary accession number(s): P13030, Q2M9V1
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: October 7, 2020
This is version 139 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, 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
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