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Protein

Tyrosine--tRNA ligase

Gene

YARS

Organism
Acanthamoeba polyphaga mimivirus (APMV)
Status
Reviewed-Annotation score: Annotation score: 3 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).By similarity2 Publications

Catalytic activityi

ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr).1 Publication

Kineticsi

  1. KM=0.5 µM for tRNA-Tyr1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei233 – 2331ATPBy similarity

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • identical protein binding Source: IntAct
    • tyrosine-tRNA ligase activity Source: UniProtKB-EC

    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. 9231.

    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:YARS
    Ordered Locus Names:MIMI_L124
    OrganismiAcanthamoeba polyphaga mimivirus (APMV)
    Taxonomic identifieri212035 [NCBI]
    Taxonomic lineageiVirusesdsDNA viruses, no RNA stageMimiviridaeMimivirus
    Virus hostiAcanthamoeba polyphaga (Amoeba) [TaxID: 5757]
    Proteomesi
    • UP000001134 Componenti: Genome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 346346Tyrosine--tRNA ligasePRO_0000055677Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-8356905,EBI-8356905

    GO - Molecular functioni

    • identical protein binding Source: IntAct

    Protein-protein interaction databases

    MINTiMINT-8411643.

    Structurei

    Secondary structure

    1
    346
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1712Combined sources
    Beta strandi21 – 244Combined sources
    Helixi26 – 3510Combined sources
    Beta strandi39 – 457Combined sources
    Helixi53 – 6816Combined sources
    Beta strandi71 – 777Combined sources
    Helixi79 – 846Combined sources
    Helixi87 – 904Combined sources
    Helixi92 – 10817Combined sources
    Helixi113 – 1153Combined sources
    Beta strandi116 – 1205Combined sources
    Helixi121 – 1277Combined sources
    Helixi129 – 14719Combined sources
    Helixi169 – 17911Combined sources
    Beta strandi186 – 1883Combined sources
    Helixi192 – 1943Combined sources
    Helixi195 – 20713Combined sources
    Beta strandi214 – 2185Combined sources
    Helixi236 – 2383Combined sources
    Helixi246 – 25510Combined sources
    Beta strandi260 – 2623Combined sources
    Helixi266 – 2738Combined sources
    Helixi275 – 2795Combined sources
    Beta strandi282 – 2843Combined sources
    Beta strandi287 – 2915Combined sources
    Helixi292 – 2998Combined sources
    Helixi304 – 32522Combined sources
    Helixi329 – 3313Combined sources
    Helixi332 – 3409Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2J5BX-ray2.20A/B2-346[»]
    DisProtiDP00726.
    ProteinModelPortaliQ5UPJ7.
    SMRiQ5UPJ7. Positions 5-342.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5UPJ7.

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi47 – 5610"HIGH" region
    Motifi230 – 2345"KMSKS" region

    Sequence similaritiesi

    Phylogenomic databases

    KOiK01866.

    Family and domain databases

    Gene3Di3.40.50.620. 1 hit.
    InterProiIPR002305. aa-tRNA-synth_Ic.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR023617. Tyr-tRNA-ligase_arc/euk-type.
    [Graphical view]
    PfamiPF00579. tRNA-synt_1b. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006588. TyrRS_arch_euk. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q5UPJ7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MENTDHTNNE HRLTQLLSIA EECETLDRLK QLVDSGRIFT AYNGFEPSGR
    60 70 80 90 100
    IHIAQALITV MNTNNIIECG GQMIIYIADW FAKMNLKMNG DINKIRELGR
    110 120 130 140 150
    YFIEVFKACG INLDGTRFIW ASEFIASNPS YIERMLDIAE FSTISRVKRC
    160 170 180 190 200
    CQIMGRNESD CLKASQIFYP CMQAADVFEL VPEGIDICQL GIDQRKVNML
    210 220 230 240 250
    AIEYANDRGL KIPISLSHHM LMSLSGPKKK MSKSDPQGAI FMDDTEQEVS
    260 270 280 290 300
    EKISRAYCTD ETFDNPIFEY IKYLLLRWFG TLNLCGKIYT DIESIQEDFS
    310 320 330 340
    SMNKRELKTD VANYINTIID LVREHFKKPE LSELLSNVKS YQQPSK
    Length:346
    Mass (Da):39,723
    Last modified:December 7, 2004 - v1
    Checksum:i43C8D8C3ECBC87B0
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY653733 Genomic DNA. Translation: AAV50399.1.
    RefSeqiYP_003986615.1. NC_014649.1.

    Genome annotation databases

    GeneIDi9924723.
    KEGGivg:9924723.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY653733 Genomic DNA. Translation: AAV50399.1.
    RefSeqiYP_003986615.1. NC_014649.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2J5BX-ray2.20A/B2-346[»]
    DisProtiDP00726.
    ProteinModelPortaliQ5UPJ7.
    SMRiQ5UPJ7. Positions 5-342.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    MINTiMINT-8411643.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    GeneIDi9924723.
    KEGGivg:9924723.

    Phylogenomic databases

    KOiK01866.

    Enzyme and pathway databases

    BRENDAi6.1.1.1. 9231.

    Miscellaneous databases

    EvolutionaryTraceiQ5UPJ7.

    Family and domain databases

    Gene3Di3.40.50.620. 1 hit.
    InterProiIPR002305. aa-tRNA-synth_Ic.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR023617. Tyr-tRNA-ligase_arc/euk-type.
    [Graphical view]
    PfamiPF00579. tRNA-synt_1b. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006588. TyrRS_arch_euk. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], FUNCTION.
      Strain: Rowbotham-Bradford.
    2. "Mimivirus TyrRS: preliminary structural and functional characterization of the first amino-acyl tRNA synthetase found in a virus."
      Abergel C., Chenivesse S., Byrne D., Suhre K., Arondel V., Claverie J.-M.
      Acta Crystallogr. F 61:212-215(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION, FUNCTION.
    3. "Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of Mimivirus TyrRS and MetRS."
      Abergel C., Rudinger-Thirion J., Giege R., Claverie J.-M.
      J. Virol. 81:12406-12417(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT, CATALYTIC ACTIVITY, KINETIC PARAMETERS.

    Entry informationi

    Entry nameiSYY_MIMIV
    AccessioniPrimary (citable) accession number: Q5UPJ7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 13, 2005
    Last sequence update: December 7, 2004
    Last modified: December 9, 2015
    This is version 65 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.