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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei34 – 341TyrosineBy similarity
    Binding sitei169 – 1691TyrosineBy similarity
    Binding sitei173 – 1731TyrosineBy similarity
    Binding sitei233 – 2331ATPBy similarity

    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi40 – 401T → A: Destabilizes the transition states for both steps of the reaction. 1 Publication
    Mutagenesisi45 – 451H → A: Does not affect the second step of the reaction. 2 Publications
    Mutagenesisi45 – 451H → 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 Publications
    Mutagenesisi48 – 481H → A: Does not affect the second step of the reaction. 1 Publication
    Mutagenesisi78 – 781D → 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 Publication
    Mutagenesisi82 – 821K → A: Destabilizes the transition states for both steps of the reaction. 1 Publication
    Mutagenesisi86 – 861R → A: Destabilizes the transition states for both steps of the reaction. 1 Publication
    Mutagenesisi152 – 1521E → 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 Publication
    Mutagenesisi152 – 1521E → D: Does not charge tRNA(Phe) in vitro with tyrosine. 1 Publication
    Mutagenesisi152 – 1521E → Q: Mischarges tRNA(Phe) with tyrosine in vitro but this mutation is not toxic in vivo. 1 Publication
    Mutagenesisi169 – 1691Y → 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 Publication
    Mutagenesisi173 – 1731Q → A: Destabilizes the transition state for the second step of the reaction. 1 Publication
    Mutagenesisi194 – 1941D → A: Destabilizes the transition state for the first step of the reaction, but does not affect the transition state for the second step. 1 Publication
    Mutagenesisi195 – 1951Q → A: Destabilizes the transition state for the first step of the reaction, but does not affect the transition state for the second step. 1 Publication
    Mutagenesisi224 – 2241T → A: Is not toxic in itself. Enhances the toxicity; when associated with A-152. 1 Publication
    Mutagenesisi230 – 2301K → A: Decreases the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication
    Mutagenesisi231 – 2311F → L: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication
    Mutagenesisi232 – 2321G → A: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication
    Mutagenesisi233 – 2331K → A: Decreases the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication
    Mutagenesisi234 – 2341T → A: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. 1 Publication
    Mutagenesisi322 – 3221L → P: 50-fold decrease in charging of tRNA(Tyr) with tyrosine. 1 Publication
    Mutagenesisi323 – 3231F → A: 90-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. 1 Publication
    Mutagenesisi323 – 3231F → L: 67-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. 1 Publication
    Mutagenesisi323 – 3231F → W: Weak decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. 1 Publication
    Mutagenesisi323 – 3231F → Y: 3-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. 1 Publication
    Mutagenesisi324 – 3241S → A: 2-fold increase in charging of tRNA(Tyr) with tyrosine. 1 Publication
    Mutagenesisi325 – 3251G → A: 5-fold increase in charging of tRNA(Tyr) with tyrosine. 1 Publication
    Mutagenesisi339 – 3391F → L: Has no effect on charging of tRNA(Tyr) with tyrosine. 1 Publication
    Mutagenesisi410 – 4101K → N: Decreases the binding of tRNA(Tyr), without affecting the formation of Tyr-AMP. Abolishes the toxicity; when associated with A-152. 1 Publication
    Mutagenesisi411 – 4111K → N: Decreases the binding of tRNA(Tyr), without affecting the formation of Tyr-AMP. Abolishes the toxicity; when associated with A-152. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 419419Tyrosine--tRNA ligasePRO_0000055642Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.

    Structurei

    Secondary structure

    1
    419
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi2 – 109Combined sources
    Beta strandi14 – 174Combined sources
    Helixi19 – 2810Combined sources
    Beta strandi32 – 376Combined sources
    Beta strandi40 – 434Combined sources
    Helixi46 – 483Combined sources
    Helixi49 – 6012Combined sources
    Beta strandi64 – 696Combined sources
    Helixi73 – 753Combined sources
    Helixi91 – 10515Combined sources
    Helixi106 – 1083Combined sources
    Beta strandi114 – 1163Combined sources
    Beta strandi119 – 1224Combined sources
    Helixi124 – 1274Combined sources
    Helixi132 – 1387Combined sources
    Helixi140 – 1423Combined sources
    Helixi145 – 1495Combined sources
    Helixi152 – 1554Combined sources
    Turni156 – 1605Combined sources
    Helixi164 – 18421Combined sources
    Beta strandi186 – 1927Combined sources
    Helixi193 – 1953Combined sources
    Helixi196 – 21015Combined sources
    Beta strandi216 – 2205Combined sources
    Beta strandi235 – 2384Combined sources
    Beta strandi240 – 2423Combined sources
    Turni243 – 2453Combined sources
    Helixi248 – 2569Combined sources
    Helixi260 – 27011Combined sources
    Helixi275 – 28713Combined sources
    Turni289 – 2913Combined sources
    Helixi293 – 30715Combined sources
    Helixi309 – 31810Combined sources
    Beta strandi325 – 3273Combined sources
    Helixi332 – 3398Combined sources
    Beta strandi344 – 3474Combined sources
    Helixi354 – 3618Combined sources
    Helixi367 – 3759Combined sources
    Beta strandi379 – 3813Combined sources
    Turni389 – 3913Combined sources
    Turni396 – 3983Combined sources
    Beta strandi399 – 40810Combined sources
    Beta strandi413 – 4186Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-319, 321-419.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00952.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini352 – 41968S4 RNA-bindingAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi39 – 4810"HIGH" region
    Motifi230 – 2345"KMSKS" region

    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.
    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_LDNU01000028.1.

    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_LDNU01000028.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-319, 321-419.
    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.
    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...

    Publicationsi

    1. "The amino acid sequence of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus."
      Winter G., Koch G.L.E., Hartley B.S., Barker D.G.
      Eur. J. Biochem. 132:383-387(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "A transcription terminator in the 5' non-coding region of the tyrosyl tRNA synthetase gene from Bacillus stearothermophilus."
      Waye M.M.Y., Winter G.
      Eur. J. Biochem. 158:505-510(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-11.
    3. "Deletion mutagenesis using an 'M13 splint': the N-terminal structural domain of tyrosyl-tRNA synthetase (B. stearothermophilus) catalyses the formation of tyrosyl adenylate."
      Waye M.M.Y., Winter G., Wilkinson A.J., Fersht A.R.
      EMBO J. 2:1827-1829(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
    4. "Construction of heterodimer tyrosyl-tRNA synthetase shows tRNATyr interacts with both subunits."
      Carter P., Bedouelle H., Winter G.
      Proc. Natl. Acad. Sci. U.S.A. 83:1189-1192(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH TRNA(TYR).
    5. "Role of residue Glu152 in the discrimination between transfer RNAs by tyrosyl-tRNA synthetase from Bacillus stearothermophilus."
      Vidal-Cros A., Bedouelle H.
      J. Mol. Biol. 223:801-810(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF HIS-45; GLU-152; THR-224; LYS-410 AND LYS-411.
    6. "The 'KMSKS' motif in tyrosyl-tRNA synthetase participates in the initial binding of tRNA(Tyr)."
      Xin Y., Li W., First E.A.
      Biochemistry 39:340-347(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-230; PHE-231; GLY-232; LYS-233 AND THR-234.
    7. "Correlating amino acid conservation with function in tyrosyl-tRNA synthetase."
      Xin Y., Li W., Dwyer D.S., First E.A.
      J. Mol. Biol. 303:287-298(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF THR-40; HIS-45; HIS-48; LYS-82 AND ARG-86.
    8. "Stabilization of the transition state for the transfer of tyrosine to tRNA(Tyr) by tyrosyl-tRNA synthetase."
      Xin Y., Li W., First E.A.
      J. Mol. Biol. 303:299-310(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASP-78; TYR-169; GLN-173; ASP-194 AND GLN-195.
    9. "An essential residue in the flexible peptide linking the two idiosynchratic domains of bacterial tyrosyl-tRNA synthetases."
      Gaillard C., Bedouelle H.
      Biochemistry 40:7192-7199(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LEU-322; PHE-323; SER-324; GLY-325 AND PHE-339.
    10. "Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold."
      Bhat T.N., Blow D.M., Brick P., Nyborg J.
      J. Mol. Biol. 158:699-709(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
    11. "Structure of tyrosyl-tRNA synthetase refined at 2.3-A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate."
      Brick P., Bhat T.N., Blow D.M.
      J. Mol. Biol. 208:83-98(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).

    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 11, 2015
    This is version 111 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.