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Protein

Tyrosine--tRNA ligase

Gene

tyrS

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
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).

Catalytic activityi

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

Kineticsi

  1. KM=1.35 mM for ATP1 Publication
  2. KM=1.8 µM for tyrosine1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei34TyrosineBy similarity1
    Binding sitei169TyrosineBy similarity1
    Binding sitei173TyrosineBy similarity1
    Binding sitei233ATPBy similarity1

    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, RNA-binding

    Enzyme and pathway databases

    BRENDAi6.1.1.1. 623.

    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
    OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
    Taxonomic identifieri1422 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi40T → A: Destabilizes the transition states for both steps of the reaction. 1 Publication1
    Mutagenesisi45H → A: Does not affect the second step of the reaction. 2 Publications1
    Mutagenesisi45H → N: Decreases the rate of formation of Tyr-AMP and, as a consequence, abolishes the aminoacylation activity. Strongly increases the toxicity; when associated with A-152. 2 Publications1
    Mutagenesisi48H → A: Does not affect the second step of the reaction. 1 Publication1
    Mutagenesisi78D → A: Does not affect the initial binding of tRNA(Tyr) and the stability of the transition state for the second step of the reaction. 1 Publication1
    Mutagenesisi82K → A: Destabilizes the transition states for both steps of the reaction. 1 Publication1
    Mutagenesisi86R → A: Destabilizes the transition states for both steps of the reaction. 1 Publication1
    Mutagenesisi152E → A: Mischarges tRNA(Phe) with tyrosine in vitro. Toxic for the cell, probably because it alters the discrimination of TyrRS against non-cognate tRNAs. The toxicity is abolished; when associated with N-410 or N-411. Strongly increases toxicity; when associated with N-45. Enhances the toxicity; when associated with A-224. 1 Publication1
    Mutagenesisi152E → D: Does not charge tRNA(Phe) in vitro with tyrosine. 1 Publication1
    Mutagenesisi152E → Q: Mischarges tRNA(Phe) with tyrosine in vitro but this mutation is not toxic in vivo. 1 Publication1
    Mutagenesisi169Y → A: Does not affect the initial binding of tRNA(Tyr) and the stability of the transition state for the second step of the reaction. 1 Publication1
    Mutagenesisi173Q → A: Destabilizes the transition state for the second step of the reaction. 1 Publication1
    Mutagenesisi194D → A: Destabilizes the transition state for the first step of the reaction, but does not affect the transition state for the second step. 1 Publication1
    Mutagenesisi195Q → A: Destabilizes the transition state for the first step of the reaction, but does not affect the transition state for the second step. 1 Publication1
    Mutagenesisi224T → A: Is not toxic in itself. Enhances the toxicity; when associated with A-152. 1 Publication1
    Mutagenesisi230K → A: Decreases the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication1
    Mutagenesisi231F → L: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication1
    Mutagenesisi232G → A: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication1
    Mutagenesisi233K → A: Decreases the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication1
    Mutagenesisi234T → A: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication1
    Mutagenesisi322L → P: 50-fold decrease in charging of tRNA(Tyr) with tyrosine. 1 Publication1
    Mutagenesisi323F → A: 90-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. 1 Publication1
    Mutagenesisi323F → L: 67-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. 1 Publication1
    Mutagenesisi323F → W: Weak decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. 1 Publication1
    Mutagenesisi323F → Y: 3-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. 1 Publication1
    Mutagenesisi324S → A: 2-fold increase in charging of tRNA(Tyr) with tyrosine. 1 Publication1
    Mutagenesisi325G → A: 5-fold increase in charging of tRNA(Tyr) with tyrosine. 1 Publication1
    Mutagenesisi339F → L: Has no effect on charging of tRNA(Tyr) with tyrosine. 1 Publication1
    Mutagenesisi410K → N: Decreases the binding of tRNA(Tyr), without affecting the formation of Tyr-AMP. Abolishes the toxicity; when associated with A-152. 1 Publication1
    Mutagenesisi411K → N: Decreases the binding of tRNA(Tyr), without affecting the formation of Tyr-AMP. Abolishes the toxicity; when associated with A-152. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000556421 – 419Tyrosine--tRNA ligaseAdd BLAST419

    Interactioni

    Subunit structurei

    Homodimer.

    Structurei

    Secondary structure

    1419
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi2 – 10Combined sources9
    Beta strandi14 – 17Combined sources4
    Helixi19 – 28Combined sources10
    Beta strandi32 – 37Combined sources6
    Beta strandi40 – 43Combined sources4
    Helixi46 – 48Combined sources3
    Helixi49 – 60Combined sources12
    Beta strandi64 – 69Combined sources6
    Helixi73 – 75Combined sources3
    Helixi91 – 105Combined sources15
    Helixi106 – 108Combined sources3
    Beta strandi114 – 116Combined sources3
    Beta strandi119 – 122Combined sources4
    Helixi124 – 127Combined sources4
    Helixi132 – 138Combined sources7
    Helixi140 – 142Combined sources3
    Helixi145 – 149Combined sources5
    Helixi152 – 155Combined sources4
    Turni156 – 160Combined sources5
    Helixi164 – 184Combined sources21
    Beta strandi186 – 192Combined sources7
    Helixi193 – 195Combined sources3
    Helixi196 – 210Combined sources15
    Beta strandi216 – 220Combined sources5
    Beta strandi235 – 238Combined sources4
    Beta strandi240 – 242Combined sources3
    Turni243 – 245Combined sources3
    Helixi248 – 256Combined sources9
    Helixi260 – 270Combined sources11
    Helixi275 – 287Combined sources13
    Turni289 – 291Combined sources3
    Helixi293 – 307Combined sources15
    Helixi309 – 318Combined sources10
    Beta strandi325 – 327Combined sources3
    Helixi332 – 339Combined sources8
    Beta strandi344 – 347Combined sources4
    Helixi354 – 361Combined sources8
    Helixi367 – 375Combined sources9
    Beta strandi379 – 381Combined sources3
    Turni389 – 391Combined sources3
    Turni396 – 398Combined sources3
    Beta strandi399 – 408Combined sources10
    Beta strandi413 – 418Combined sources6

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JH3NMR-A321-419[»]
    1TYAX-ray2.80E1-319[»]
    1TYBX-ray2.50E1-319[»]
    1TYCX-ray2.50A1-319[»]
    1TYDX-ray2.50E1-319[»]
    2TS1X-ray2.30A1-419[»]
    3TS1X-ray2.70A1-419[»]
    4TS1X-ray2.50A/B1-317[»]
    DisProtiDP00095.
    ProteinModelPortaliP00952.
    SMRiP00952.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00952.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini352 – 419S4 RNA-bindingAdd BLAST68

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi39 – 48"HIGH" region10
    Motifi230 – 234"KMSKS" region5

    Sequence similaritiesi

    Contains 1 S4 RNA-binding domain.Curated

    Family and domain databases

    Gene3Di3.10.290.10. 1 hit.
    3.40.50.620. 1 hit.
    HAMAPiMF_02006. Tyr_tRNA_synth_type1. 1 hit.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002305. aa-tRNA-synth_Ic.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR002942. S4_RNA-bd.
    IPR002307. Tyr-tRNA-ligase.
    IPR024088. Tyr-tRNA-ligase_bac-type.
    IPR024107. Tyr-tRNA-ligase_bac_1.
    [Graphical view]
    PANTHERiPTHR11766. PTHR11766. 1 hit.
    PfamiPF01479. S4. 1 hit.
    PF00579. tRNA-synt_1b. 1 hit.
    [Graphical view]
    PRINTSiPR01040. TRNASYNTHTYR.
    SMARTiSM00363. S4. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00234. tyrS. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    PS50889. S4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P00952-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDLLAELQWR GLVNQTTDED GLRKLLNEER VTLYCGFDPT ADSLHIGHLA
    60 70 80 90 100
    TILTMRRFQQ AGHRPIALVG GATGLIGDPS GKKSERTLNA KETVEAWSAR
    110 120 130 140 150
    IKEQLGRFLD FEADGNPAKI KNNYDWIGPL DVITFLRDVG KHFSVNYMMA
    160 170 180 190 200
    KESVQSRIET GISFTEFSYM MLQAYDFLRL YETEGCRLQI GGSDQWGNIT
    210 220 230 240 250
    AGLELIRKTK GEARAFGLTI PLVTKADGTK FGKTESGTIW LDKEKTSPYE
    260 270 280 290 300
    FYQFWINTDD RDVIRYLKYF TFLSKEEIEA LEQELREAPE KRAAQKTLAE
    310 320 330 340 350
    EVTKLVHGEE ALRQAIRISE ALFSGDIANL TAAEIEQGFK DVPSFVHEGG
    360 370 380 390 400
    DVPLVELLVS AGISPSKRQA REDIQNGAIY VNGERLQDVG AILTAEHRLE
    410
    GRFTVIRRGK KKYYLIRYA
    Length:419
    Mass (Da):47,303
    Last modified:July 21, 1986 - v1
    Checksum:iB9CB64AEEEE2010F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J01546 Genomic DNA. No translation available.
    X04193 Genomic DNA. Translation: CAA27784.1.
    PIRiA01179. SYBSYF.
    RefSeqiWP_033014498.1. NZ_LUCR01000153.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J01546 Genomic DNA. No translation available.
    X04193 Genomic DNA. Translation: CAA27784.1.
    PIRiA01179. SYBSYF.
    RefSeqiWP_033014498.1. NZ_LUCR01000153.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JH3NMR-A321-419[»]
    1TYAX-ray2.80E1-319[»]
    1TYBX-ray2.50E1-319[»]
    1TYCX-ray2.50A1-319[»]
    1TYDX-ray2.50E1-319[»]
    2TS1X-ray2.30A1-419[»]
    3TS1X-ray2.70A1-419[»]
    4TS1X-ray2.50A/B1-317[»]
    DisProtiDP00095.
    ProteinModelPortaliP00952.
    SMRiP00952.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BRENDAi6.1.1.1. 623.

    Miscellaneous databases

    EvolutionaryTraceiP00952.

    Family and domain databases

    Gene3Di3.10.290.10. 1 hit.
    3.40.50.620. 1 hit.
    HAMAPiMF_02006. Tyr_tRNA_synth_type1. 1 hit.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002305. aa-tRNA-synth_Ic.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR002942. S4_RNA-bd.
    IPR002307. Tyr-tRNA-ligase.
    IPR024088. Tyr-tRNA-ligase_bac-type.
    IPR024107. Tyr-tRNA-ligase_bac_1.
    [Graphical view]
    PANTHERiPTHR11766. PTHR11766. 1 hit.
    PfamiPF01479. S4. 1 hit.
    PF00579. tRNA-synt_1b. 1 hit.
    [Graphical view]
    PRINTSiPR01040. TRNASYNTHTYR.
    SMARTiSM00363. S4. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00234. tyrS. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    PS50889. S4. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiSYY_GEOSE
    AccessioniPrimary (citable) accession number: P00952
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 21, 1986
    Last modified: November 2, 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

    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.