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Protein

Tyrosine--tRNA ligase

Gene

tyrS

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).1 Publication

Catalytic activityi

ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr).

Kineticsi

  1. KM=15 µM for tRNA(Tyr) (at 45 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei32 – 321Tyrosine1 Publication
    Binding sitei36 – 361Tyrosine1 Publication
    Binding sitei173 – 1731Tyrosine1 Publication
    Binding sitei207 – 2071ATPSequence analysis

    GO - Molecular functioni

    GO - Biological processi

    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

    BRENDAi6.1.1.1. 3260.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Tyrosine--tRNA ligase (EC:6.1.1.1)
    Alternative name(s):
    Tyrosyl-tRNA synthetase
    Short name:
    TyrRS
    Gene namesi
    Name:tyrS
    Ordered Locus Names:MJ0389
    OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
    Taxonomic identifieri243232 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
    Proteomesi
    • UP000000805 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi32 – 321Y → Q: Confers specificity for the non-natural amino acid O-methyl-tyrosine; when associated with T-107; A-158 and P-162.
    Mutagenesisi107 – 1071E → T: Confers specificity for the non-natural amino acid O-methyl-tyrosine; when associated with Q-32; A-158 and P-162.
    Mutagenesisi158 – 1581D → A: Confers specificity for the non-natural amino acid O-methyl-tyrosine; when associated with Q-32; T-107 and P-162.
    Mutagenesisi162 – 1621L → P: Confers specificity for the non-natural amino acid O-methyl-tyrosine; when associated with Q-32; T-107 and A-158.
    Mutagenesisi286 – 2861D → A: Decreases the rate of aminoacylation more than 10-fold, without effect on tyrosyl adenylate synthesis. 2 Publications
    Mutagenesisi286 – 2861D → R: Decreases the rate of aminoacylation with wild-type tRNA and increases aminoacylation with amber suppressor tRNA 8-fold. Decreases affinity for wild-type tRNA and increases affinity for amber suppressor tRNA. 2 Publications
    Mutagenesisi288 – 2881K → A: Decreases the rate of aminoacylation more than 200-fold, without effect on tyrosyl adenylate synthesis. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 306306Tyrosine--tRNA ligasePRO_0000055669Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei143 – 1431Interaction with t-RNA

    Protein-protein interaction databases

    STRINGi243232.MJ_0389.

    Structurei

    Secondary structure

    1
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 86Combined sources
    Beta strandi12 – 154Combined sources
    Helixi17 – 248Combined sources
    Beta strandi26 – 3510Combined sources
    Helixi43 – 5715Combined sources
    Beta strandi60 – 667Combined sources
    Helixi68 – 736Combined sources
    Helixi79 – 9517Combined sources
    Beta strandi101 – 1044Combined sources
    Helixi105 – 1073Combined sources
    Turni108 – 1103Combined sources
    Helixi112 – 12413Combined sources
    Helixi127 – 1337Combined sources
    Turni134 – 1374Combined sources
    Helixi147 – 16216Combined sources
    Beta strandi165 – 1706Combined sources
    Helixi171 – 1733Combined sources
    Helixi174 – 18310Combined sources
    Beta strandi184 – 1863Combined sources
    Beta strandi189 – 1935Combined sources
    Beta strandi201 – 2044Combined sources
    Turni207 – 2104Combined sources
    Beta strandi214 – 2163Combined sources
    Helixi219 – 22810Combined sources
    Helixi240 – 2489Combined sources
    Beta strandi251 – 2555Combined sources
    Helixi259 – 2613Combined sources
    Beta strandi265 – 2695Combined sources
    Helixi270 – 2789Combined sources
    Helixi284 – 30623Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1J1UX-ray1.95A1-306[»]
    1U7DX-ray2.65A/B1-306[»]
    1U7XX-ray3.00A/B1-306[»]
    1ZH0X-ray1.90A1-306[»]
    1ZH6X-ray2.50A1-306[»]
    2AG6X-ray1.90A1-306[»]
    2HGZX-ray2.50A2-306[»]
    2PXHX-ray1.97A1-306[»]
    2ZP1X-ray1.70A1-306[»]
    3D6UX-ray2.20A1-306[»]
    3D6VX-ray2.20A1-306[»]
    3N2YX-ray2.49A/B1-306[»]
    3QE4X-ray2.30A/B1-306[»]
    4HJRX-ray2.50A/B1-306[»]
    4HJXX-ray2.91A/B1-306[»]
    4HK4X-ray2.30A1-306[»]
    4HPWX-ray2.00A1-306[»]
    4ND6X-ray2.00A1-306[»]
    4ND7X-ray2.00A1-306[»]
    4NDAX-ray1.70A1-306[»]
    4NX2X-ray2.00A1-306[»]
    4PBRX-ray1.90A1-306[»]
    4PBSX-ray2.01A1-306[»]
    4PBTX-ray1.90A1-306[»]
    ProteinModelPortaliQ57834.
    SMRiQ57834. Positions 1-306.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ57834.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni151 – 1588Tyrosine
    Regioni228 – 2314Interaction with t-RNA
    Regioni283 – 2886Interaction with t-RNA

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi37 – 459"HIGH" region
    Motifi204 – 2085"KMSKS" region

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiarCOG01886. Archaea.
    COG0162. LUCA.
    InParanoidiQ57834.
    KOiK01866.
    OMAiFEYHVFP.
    PhylomeDBiQ57834.

    Family and domain databases

    Gene3Di3.40.50.620. 1 hit.
    HAMAPiMF_02008. Tyr_tRNA_synth_type3.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002305. aa-tRNA-synth_Ic.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR002307. Tyr-tRNA-ligase.
    IPR023684. Tyr-tRNA-ligase_3.
    IPR023617. Tyr-tRNA-ligase_arc/euk-type.
    [Graphical view]
    PfamiPF00579. tRNA-synt_1b. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006588. TyrRS_arch_euk. 1 hit.
    PRINTSiPR01040. TRNASYNTHTYR.
    TIGRFAMsiTIGR00234. tyrS. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q57834-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDEFEMIKRN TSEIISEEEL REVLKKDEKS AYIGFEPSGK IHLGHYLQIK
    60 70 80 90 100
    KMIDLQNAGF DIIILLADLH AYLNQKGELD EIRKIGDYNK KVFEAMGLKA
    110 120 130 140 150
    KYVYGSEFQL DKDYTLNVYR LALKTTLKRA RRSMELIARE DENPKVAEVI
    160 170 180 190 200
    YPIMQVNDIH YLGVDVAVGG MEQRKIHMLA RELLPKKVVC IHNPVLTGLD
    210 220 230 240 250
    GEGKMSSSKG NFIAVDDSPE EIRAKIKKAY CPAGVVEGNP IMEIAKYFLE
    260 270 280 290 300
    YPLTIKRPEK FGGDLTVNSY EELESLFKNK ELHPMDLKNA VAEELIKILE

    PIRKRL
    Length:306
    Mass (Da):35,049
    Last modified:November 1, 1997 - v1
    Checksum:i1887760ABAF2DD5E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB98375.1.
    PIRiE64348.

    Genome annotation databases

    EnsemblBacteriaiAAB98375; AAB98375; MJ_0389.
    KEGGimja:MJ_0389.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB98375.1.
    PIRiE64348.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1J1UX-ray1.95A1-306[»]
    1U7DX-ray2.65A/B1-306[»]
    1U7XX-ray3.00A/B1-306[»]
    1ZH0X-ray1.90A1-306[»]
    1ZH6X-ray2.50A1-306[»]
    2AG6X-ray1.90A1-306[»]
    2HGZX-ray2.50A2-306[»]
    2PXHX-ray1.97A1-306[»]
    2ZP1X-ray1.70A1-306[»]
    3D6UX-ray2.20A1-306[»]
    3D6VX-ray2.20A1-306[»]
    3N2YX-ray2.49A/B1-306[»]
    3QE4X-ray2.30A/B1-306[»]
    4HJRX-ray2.50A/B1-306[»]
    4HJXX-ray2.91A/B1-306[»]
    4HK4X-ray2.30A1-306[»]
    4HPWX-ray2.00A1-306[»]
    4ND6X-ray2.00A1-306[»]
    4ND7X-ray2.00A1-306[»]
    4NDAX-ray1.70A1-306[»]
    4NX2X-ray2.00A1-306[»]
    4PBRX-ray1.90A1-306[»]
    4PBSX-ray2.01A1-306[»]
    4PBTX-ray1.90A1-306[»]
    ProteinModelPortaliQ57834.
    SMRiQ57834. Positions 1-306.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243232.MJ_0389.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAB98375; AAB98375; MJ_0389.
    KEGGimja:MJ_0389.

    Phylogenomic databases

    eggNOGiarCOG01886. Archaea.
    COG0162. LUCA.
    InParanoidiQ57834.
    KOiK01866.
    OMAiFEYHVFP.
    PhylomeDBiQ57834.

    Enzyme and pathway databases

    BRENDAi6.1.1.1. 3260.

    Miscellaneous databases

    EvolutionaryTraceiQ57834.

    Family and domain databases

    Gene3Di3.40.50.620. 1 hit.
    HAMAPiMF_02008. Tyr_tRNA_synth_type3.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002305. aa-tRNA-synth_Ic.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR002307. Tyr-tRNA-ligase.
    IPR023684. Tyr-tRNA-ligase_3.
    IPR023617. Tyr-tRNA-ligase_arc/euk-type.
    [Graphical view]
    PfamiPF00579. tRNA-synt_1b. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006588. TyrRS_arch_euk. 1 hit.
    PRINTSiPR01040. TRNASYNTHTYR.
    TIGRFAMsiTIGR00234. tyrS. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
    2. "Major anticodon-binding region missing from an archaebacterial tRNA synthetase."
      Steer B.A., Schimmel P.
      J. Biol. Chem. 274:35601-35606(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT, KINETIC PARAMETERS.
    3. "Domain-domain communication in a miniature archaebacterial tRNA synthetase."
      Steer B.A., Schimmel P.
      Proc. Natl. Acad. Sci. U.S.A. 96:13644-13649(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASP-286 AND LYS-288.
    4. "Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion."
      Kobayashi T., Nureki O., Ishitani R., Yaremchuk A., Tukalo M., Cusack S., Sakamoto K., Yokoyama S.
      Nat. Struct. Biol. 10:425-432(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH TRNA(TYR) AND TYROSINE, MUTAGENESIS OF ASP-286, SUBUNIT.
    5. "Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine."
      Zhang Y., Wang L., Schultz P.G., Wilson I.A.
      Protein Sci. 14:1340-1349(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.66 ANGSTROMS) OF WILD-TYPE AND O-METHYL-TYROSINE-SPECIFIC MUTANT APOENZYME.

    Entry informationi

    Entry nameiSYY_METJA
    AccessioniPrimary (citable) accession number: Q57834
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: February 17, 2016
    This is version 114 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. Methanococcus jannaschii
      Methanococcus jannaschii: entries and gene names
    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.