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Protein

Serine--tRNA ligase

Gene

serS

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

Functioni

Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).3 Publications

Catalytic activityi

ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec).

Kineticsi

  1. KM=64 µM for serine2 Publications
  2. KM=0.068 µM for ATP2 Publications

    Pathwayi: selenocysteinyl-tRNA(Sec) biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes L-seryl-tRNA(Sec) from L-serine and tRNA(Sec).
    Proteins known to be involved in this subpathway in this organism are:
    1. Serine--tRNA ligase (serS)
    This subpathway is part of the pathway selenocysteinyl-tRNA(Sec) biosynthesis, which is itself part of Aminoacyl-tRNA biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-seryl-tRNA(Sec) from L-serine and tRNA(Sec), the pathway selenocysteinyl-tRNA(Sec) biosynthesis and in Aminoacyl-tRNA biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei291 – 2911SerineBy similarity
    Binding sitei391 – 3911SerineBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi268 – 2703ATPBy similarity
    Nucleotide bindingi355 – 3584ATPBy similarity

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-HAMAP
    • identical protein binding Source: IntAct
    • magnesium ion binding Source: EcoCyc
    • serine-tRNA ligase activity Source: UniProtKB

    GO - Biological processi

    • selenocysteine biosynthetic process Source: EcoCyc
    • selenocysteinyl-tRNA(Sec) biosynthetic process Source: UniProtKB-UniPathway
    • seryl-tRNA aminoacylation Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:SERS-MONOMER.
    ECOL316407:JW0876-MONOMER.
    MetaCyc:SERS-MONOMER.
    UniPathwayiUPA00906; UER00895.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Serine--tRNA ligase (EC:6.1.1.11)
    Alternative name(s):
    Seryl-tRNA synthetase
    Short name:
    SerRS
    Seryl-tRNA(Ser/Sec) synthetase
    Gene namesi
    Name:serS
    Ordered Locus Names:b0893, JW0876
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10947. serS.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi355 – 3551E → Q: Loss of serine activation activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 430430Serine--tRNA ligasePRO_0000122044Add
    BLAST

    Proteomic databases

    EPDiP0A8L1.
    PaxDbiP0A8L1.
    PRIDEiP0A8L1.

    2D gel databases

    SWISS-2DPAGEP0A8L1.

    Interactioni

    Subunit structurei

    Homodimer. The tRNA molecule binds across the dimer.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-548422,EBI-548422

    GO - Molecular functioni

    • identical protein binding Source: IntAct

    Protein-protein interaction databases

    BioGridi4261485. 9 interactions.
    DIPiDIP-35989N.
    IntActiP0A8L1. 16 interactions.
    MINTiMINT-1230011.
    STRINGi511145.b0893.

    Structurei

    3D structure databases

    ProteinModelPortaliP0A8L1.
    SMRiP0A8L1. Positions 1-423.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni237 – 2393Serine bindingBy similarity

    Domaini

    Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding.2 Publications

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CGR. Bacteria.
    COG0172. LUCA.
    HOGENOMiHOG000035938.
    InParanoidiP0A8L1.
    KOiK01875.
    OMAiYRPERHE.
    OrthoDBiEOG61KBH9.
    PhylomeDBiP0A8L1.

    Family and domain databases

    Gene3Di1.10.287.40. 1 hit.
    HAMAPiMF_00176. Ser_tRNA_synth_type1.
    InterProiIPR002314. aa-tRNA-synt_IIb.
    IPR006195. aa-tRNA-synth_II.
    IPR002317. Ser-tRNA-ligase_type_1.
    IPR015866. Ser-tRNA-synth_1_N.
    IPR010978. tRNA-bd_arm.
    [Graphical view]
    PANTHERiPTHR11778. PTHR11778. 1 hit.
    PfamiPF02403. Seryl_tRNA_N. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
    PRINTSiPR00981. TRNASYNTHSER.
    SUPFAMiSSF46589. SSF46589. 1 hit.
    TIGRFAMsiTIGR00414. serS. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0A8L1-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLDPNLLRNE PDAVAEKLAR RGFKLDVDKL GALEERRKVL QVKTENLQAE
    60 70 80 90 100
    RNSRSKSIGQ AKARGEDIEP LRLEVNKLGE ELDAAKAELD ALQAEIRDIA
    110 120 130 140 150
    LTIPNLPADE VPVGKDENDN VEVSRWGTPR EFDFEVRDHV TLGEMHSGLD
    160 170 180 190 200
    FAAAVKLTGS RFVVMKGQIA RMHRALSQFM LDLHTEQHGY SENYVPYLVN
    210 220 230 240 250
    QDTLYGTGQL PKFAGDLFHT RPLEEEADTS NYALIPTAEV PLTNLVRGEI
    260 270 280 290 300
    IDEDDLPIKM TAHTPCFRSE AGSYGRDTRG LIRMHQFDKV EMVQIVRPED
    310 320 330 340 350
    SMAALEEMTG HAEKVLQLLG LPYRKIILCT GDMGFGACKT YDLEVWIPAQ
    360 370 380 390 400
    NTYREISSCS NVWDFQARRM QARCRSKSDK KTRLVHTLNG SGLAVGRTLV
    410 420 430
    AVMENYQQAD GRIEVPEVLR PYMNGLEYIG
    Length:430
    Mass (Da):48,414
    Last modified:June 7, 2005 - v1
    Checksum:i87675745A512A626
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X05017 Genomic DNA. Translation: CAA28673.1.
    U00096 Genomic DNA. Translation: AAC73979.1.
    AP009048 Genomic DNA. Translation: BAA35625.1.
    J03412 Genomic DNA. Translation: AAA83842.1.
    PIRiA26400. YSEC.
    RefSeqiNP_415413.1. NC_000913.3.
    WP_000886683.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73979; AAC73979; b0893.
    BAA35625; BAA35625; BAA35625.
    GeneIDi945506.
    KEGGiecj:JW0876.
    eco:b0893.
    PATRICi32116997. VBIEscCol129921_0923.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X05017 Genomic DNA. Translation: CAA28673.1.
    U00096 Genomic DNA. Translation: AAC73979.1.
    AP009048 Genomic DNA. Translation: BAA35625.1.
    J03412 Genomic DNA. Translation: AAA83842.1.
    PIRiA26400. YSEC.
    RefSeqiNP_415413.1. NC_000913.3.
    WP_000886683.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP0A8L1.
    SMRiP0A8L1. Positions 1-423.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261485. 9 interactions.
    DIPiDIP-35989N.
    IntActiP0A8L1. 16 interactions.
    MINTiMINT-1230011.
    STRINGi511145.b0893.

    2D gel databases

    SWISS-2DPAGEP0A8L1.

    Proteomic databases

    EPDiP0A8L1.
    PaxDbiP0A8L1.
    PRIDEiP0A8L1.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73979; AAC73979; b0893.
    BAA35625; BAA35625; BAA35625.
    GeneIDi945506.
    KEGGiecj:JW0876.
    eco:b0893.
    PATRICi32116997. VBIEscCol129921_0923.

    Organism-specific databases

    EchoBASEiEB0940.
    EcoGeneiEG10947. serS.

    Phylogenomic databases

    eggNOGiENOG4105CGR. Bacteria.
    COG0172. LUCA.
    HOGENOMiHOG000035938.
    InParanoidiP0A8L1.
    KOiK01875.
    OMAiYRPERHE.
    OrthoDBiEOG61KBH9.
    PhylomeDBiP0A8L1.

    Enzyme and pathway databases

    UniPathwayiUPA00906; UER00895.
    BioCyciEcoCyc:SERS-MONOMER.
    ECOL316407:JW0876-MONOMER.
    MetaCyc:SERS-MONOMER.

    Miscellaneous databases

    PROiP0A8L1.

    Family and domain databases

    Gene3Di1.10.287.40. 1 hit.
    HAMAPiMF_00176. Ser_tRNA_synth_type1.
    InterProiIPR002314. aa-tRNA-synt_IIb.
    IPR006195. aa-tRNA-synth_II.
    IPR002317. Ser-tRNA-ligase_type_1.
    IPR015866. Ser-tRNA-synth_1_N.
    IPR010978. tRNA-bd_arm.
    [Graphical view]
    PANTHERiPTHR11778. PTHR11778. 1 hit.
    PfamiPF02403. Seryl_tRNA_N. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
    PRINTSiPR00981. TRNASYNTHSER.
    SUPFAMiSSF46589. SSF46589. 1 hit.
    TIGRFAMsiTIGR00414. serS. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Cloning and characterization of the gene for Escherichia coli seryl-tRNA synthetase."
      Haertlein M., Madern D., Leberman R.
      Nucleic Acids Res. 15:1005-1017(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    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. "Nucleotide sequence of the dmsABC operon encoding the anaerobic dimethylsulphoxide reductase of Escherichia coli."
      Bilous P.T., Cole S.T., Anderson W.F., Weiner J.H.
      Mol. Microbiol. 2:785-795(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 251-430.
    6. "Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine."
      Leinfelder W., Zehelein E., Mandrand-Berthelot M.A., Boeck A.
      Nature 331:723-725(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A SERYL-TRNA(SEC) SYNTHETASE.
    7. "Escherichia coli seryl-tRNA synthetase: the structure of a class 2 aminoacyl-tRNA synthetase."
      Leberman R., Haertlein M., Cusack S.
      Biochim. Biophys. Acta 1089:287-298(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    8. "Crystallization of the seryl-tRNA synthetase:tRNA(Ser) complex of Escherichia coli."
      Price S., Cusack S., Borel F., Berthet-Colominas C., Leberman R.
      FEBS Lett. 324:167-170(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, DOMAIN, CRYSTALLIZATION.
    9. "Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity."
      Borel F., Vincent C., Leberman R., Haertlein M.
      Nucleic Acids Res. 22:2963-2969(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, KINETIC PARAMETERS, DOMAIN.
    10. "Seryl-tRNA synthetase from Escherichia coli: functional evidence for cross-dimer tRNA binding during aminoacylation."
      Vincent C., Borel F., Willison J.C., Leberman R., Haertlein M.
      Nucleic Acids Res. 23:1113-1118(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, KINETIC PARAMETERS, MUTAGENESIS OF GLU-355, SUBUNIT, REACTION MECHANISM.
    11. "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.
    12. "A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A."
      Cusack S., Berthet-Colominas C., Haertlein M., Nassar N., Leberman R.
      Nature 347:249-255(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).

    Entry informationi

    Entry nameiSYS_ECOLI
    AccessioniPrimary (citable) accession number: P0A8L1
    Secondary accession number(s): P09156
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: June 7, 2005
    Last modified: March 16, 2016
    This is version 96 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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.