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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)DescriptionActionsGraphical viewLength
    Binding sitei233ATPBy similarity1

    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00000556771 – 346Tyrosine--tRNA ligaseAdd BLAST346

    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

    1346
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 17Combined sources12
    Beta strandi21 – 24Combined sources4
    Helixi26 – 35Combined sources10
    Beta strandi39 – 45Combined sources7
    Helixi53 – 68Combined sources16
    Beta strandi71 – 77Combined sources7
    Helixi79 – 84Combined sources6
    Helixi87 – 90Combined sources4
    Helixi92 – 108Combined sources17
    Helixi113 – 115Combined sources3
    Beta strandi116 – 120Combined sources5
    Helixi121 – 127Combined sources7
    Helixi129 – 147Combined sources19
    Helixi169 – 179Combined sources11
    Beta strandi186 – 188Combined sources3
    Helixi192 – 194Combined sources3
    Helixi195 – 207Combined sources13
    Beta strandi214 – 218Combined sources5
    Helixi236 – 238Combined sources3
    Helixi246 – 255Combined sources10
    Beta strandi260 – 262Combined sources3
    Helixi266 – 273Combined sources8
    Helixi275 – 279Combined sources5
    Beta strandi282 – 284Combined sources3
    Beta strandi287 – 291Combined sources5
    Helixi292 – 299Combined sources8
    Helixi304 – 325Combined sources22
    Helixi329 – 331Combined sources3
    Helixi332 – 340Combined sources9

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ5UPJ7.

    Family & Domainsi

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi47 – 56"HIGH" region10
    Motifi230 – 234"KMSKS" region5

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2J5BX-ray2.20A/B2-346[»]
    DisProtiDP00726.
    ProteinModelPortaliQ5UPJ7.
    SMRiQ5UPJ7.
    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...

    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: November 2, 2016
    This is version 67 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.