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Protein

Threonine--tRNA ligase

Gene

thrS

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr) (PubMed:15079065, PubMed:10881191, PubMed:18997014). The rate-limiting step is amino acid activation in the presence of tRNA (PubMed:18997014). The 2'-OH of the acceptor base (adenine 76, A76) of tRNA(Thr) and His-309 collaborate to transfer L-Thr to the tRNA; substitution of 2'-OH of A76 with hydrogen or fluorine decreases transfer efficiency 760 and 100-fold respectively (PubMed:18997014). The zinc ion in the active site discriminates against charging of the isosteric amino acid valine (PubMed:10881191). Also activates L-serine, but does not detectably transfer it to tRNA(Thr) (PubMed:15079065). Edits incorrectly charged L-seryl-tRNA(Thr) via its editing domain (PubMed:15079065, PubMed:11136973, PubMed:15525511), in a post-transfer reaction probably via water-mediated hydrolysis (PubMed:15525511).6 Publications
ThrS is also a translational repressor protein, it controls binds its own mRNA in the operator region upstream of the start codon (PubMed:3086882). The mRNA region upstream of the start codon has a tRNA-like secondary structure; mRNA and tRNA compete for binding to ThrRS (PubMed:2254931). ThrRS represses translation by preventing the ribosome from to mRNA, and tRNA(Thr) acts as an antirepressor allowing fine level control of enzyme synthesis (PubMed:2254931). X-ray structures prove that operator mRNA and tRNA bind to overlapping sites in the protein (PubMed:10319817, PubMed:11953757).4 Publications

Catalytic activityi

ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).UniRule annotation3 Publications

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit. It helps recognize and select the amino acid substrate, and thus has neither a purely catalytic or structural role (PubMed:10881191).6 Publications

Enzyme regulationi

Inhibited non-competitively by borrelidin (BN, KI is 3.7 nM) which binds in a 1:1 stoichiometry, inhibiting L-thr activation (PubMed:15507440). BN binds to 4 distinct subsites in the protein, preventing binding of all 3 substrates; BN also inhibits human ThrRS, and thus it is not useful as an antibiotic (PubMed:25824639).2 Publications

Kineticsi

kcat is 36, 22 and 26 s(-1) for L-threonine, beta-hydroxynorvaline and L-serine respectively.1 Publication
  1. KM=94 µM for ATP1 Publication
  2. KM=110 µM for L-threonine activation2 Publications
  3. KM=120 µM for L-threonine activation1 Publication
  4. KM=0.86 µM for L-threonine aminoacylation1 Publication
  5. KM=1.95 mM for beta-hydroxynorvaline activation1 Publication
  6. KM=81.5 mM for L-serine activation1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei309Binds 2'-OH of adenine 76 of tRNA(Thr), the tRNA acceptor baseCombined sources1 Publication1
    Binding sitei325Cross-subunit contacts with tRNA(Thr)1 Publication1
    Metal bindingi334ZincUniRule annotation4 Publications1
    Binding sitei363Contacts 3'-CCA of tRNA1 Publication1
    Binding sitei375Contacts 3'-CCA of tRNA1 Publication1
    Binding sitei376AMP; via amide nitrogen and carbonyl oxygenCombined sources1 Publication1
    Binding sitei379AMP1 Publication1
    Binding sitei381AMPCombined sources1 Publication1
    Metal bindingi385Zinc; via tele nitrogenUniRule annotation4 Publications1
    Binding sitei462Contacts 3'-CCA of tRNA1 Publication1
    Binding sitei484Contacts 3'-CCA of tRNA1 Publication1
    Metal bindingi511Zinc; via pros nitrogenUniRule annotation3 Publications1
    Binding sitei517AMPCombined sources1 Publication1
    Binding sitei520AMP1 Publication1
    Binding sitei589Contacts anticodon region of tRNA1 Publication1
    Binding sitei609Contacts anticodon region of tRNA1 Publication1
    Binding sitei609Contacts mRNA operator1 Publication1
    Binding sitei615Contacts mRNA operator1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi363 – 365AMPCombined sources1 Publication3
    Nucleotide bindingi479 – 480AMPCombined sources1 Publication2

    GO - Molecular functioni

    • aminoacyl-tRNA editing activity Source: EcoCyc
    • ATP binding Source: EcoliWiki
    • drug binding Source: EcoliWiki
    • ligase activity, forming aminoacyl-tRNA and related compounds Source: EcoliWiki
    • mRNA 5'-UTR binding Source: EcoCyc
    • RNA binding Source: EcoliWiki
    • threonine-tRNA ligase activity Source: EcoCyc
    • translation repressor activity, nucleic acid binding Source: EcoCyc
    • tRNA binding Source: UniProtKB-KW
    • zinc ion binding Source: EcoCyc

    GO - Biological processi

    • negative regulation of translational initiation Source: EcoCyc
    • regulation of translation Source: EcoCyc
    • response to antibiotic Source: UniProtKB-KW
    • threonyl-tRNA aminoacylation Source: EcoCyc
    • tRNA aminoacylation Source: EcoliWiki
    • tRNA aminoacylation for protein translation Source: EcoliWiki

    Keywordsi

    Molecular functionAminoacyl-tRNA synthetase, Ligase, Repressor, RNA-binding, tRNA-binding
    Biological processAntibiotic resistance, Protein biosynthesis, Translation regulation
    LigandATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:THRS-MONOMER.
    MetaCyc:THRS-MONOMER.
    BRENDAi6.1.1.3. 2026.
    SABIO-RKiP0A8M3.

    Protein family/group databases

    MoonProtiP0A8M3.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Threonine--tRNA ligaseUniRule annotation (EC:6.1.1.3UniRule annotation1 Publication)
    Alternative name(s):
    Threonyl-tRNA synthetaseUniRule annotation
    Short name:
    ThrRSUniRule annotation
    Gene namesi
    Name:thrSUniRule annotation
    Ordered Locus Names:b1719, JW1709
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11001. thrS.

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    • cytoplasm Source: EcoliWiki
    • cytosol Source: EcoCyc

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Biotechnological usei

    A number of inhibitors with high affinity for bacterial ThrRS and less affinity for human ThrRS have been identified that might make good antibiotics.1 Publication

    Disruption phenotypei

    Essential, it cannot be deleted.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi73 – 77HSCAH → ASCAA: No longer edits mischarged L-seryl-tRNA(Thr), mischarges tRNA(Thr) with L-serine, correct acylation is unaffected. 1 Publication5
    Mutagenesisi156K → A: Mischarges tRNA(Thr) with L-serine. 1 Publication1
    Mutagenesisi180D → A: No longer edits mischarged L-seryl-tRNA(Thr), mischarges tRNA(Thr) with L-serine, correct acylation is unaffected. 1 Publication1
    Mutagenesisi182C → A: Very high mischarging of tRNA(Thr) with L-serine. 1 Publication1
    Mutagenesisi186H → A: Mischarges tRNA(Thr) with L-serine. 1 Publication1
    Mutagenesisi296P → S: Confers resistance to borrelidin (BN); KM for L-Thr is unchanged, KM for ATP increases to 187 uM, KI for BN increases to 4.5 nM. 1 Publication1
    Mutagenesisi307T → A: KI for BN increases 10-fold, no change in aminoacylation activity. 1 Publication1
    Mutagenesisi309H → A: 10-fold increase in KM for Thr for activation, 240-fold decrease in aminoacyl transfer. Cells have a long lag phase and reach stationary phase at a lower cell density. KI for BN increases 1000-fold, supports growth in the presence of BN. 2 Publications1
    Mutagenesisi334C → S: Does not complement a deletion strain. 1 Publication1
    Mutagenesisi337H → A: KI for BN increases 12-fold, no change in aminoacylation activity, supports growth in the presence of BN. 1 Publication1
    Mutagenesisi363R → A: 700-fold decrease in kcat for Thr activation, 1000-fold decrease in kcat of aminoacylation, no change in KM. 1 Publication1
    Mutagenesisi381Q → A: 100-fold increase in KM for Thr for activation. 1 Publication1
    Mutagenesisi385H → A or N: Does not complement a deletion strain. 1 Publication1
    Mutagenesisi465K → A: 35-fold decrease in kcat for Thr activation, 570-fold decrease in kcat of aminoacylation, no change in KM. 1 Publication1
    Mutagenesisi479Q → A: Wild-type Thr activation and aminoacylation. 1 Publication1
    Mutagenesisi489L → M: Confers resistance to borrelidin (BN); KM for L-thr is unchanged, KM for ATP increases to 163 uM, KI for BN increases to 7.8 nM, supports growth in the presence of BN. 1 Publication1
    Mutagenesisi489L → W: KI for BN increases 1500-fold, no change in aminoacylation activity, supports growth in the presence of BN. 1 Publication1
    Mutagenesisi511H → A or N: Does not complement a deletion strain, has dominant lethal effect in presence of wild-type gene, probably due to repression of the wild-type gene. 1 Publication1
    Mutagenesisi531G → GEGK: KI for BN increases 8-fold, decreases aminoacylation activity, does not support growth in the presence of BN. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001009731 – 642Threonine--tRNA ligaseAdd BLAST642

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei286N6-acetyllysineUniRule annotation1 Publication1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    PaxDbiP0A8M3.
    PRIDEiP0A8M3.

    PTM databases

    iPTMnetiP0A8M3.

    Interactioni

    Subunit structurei

    Homodimer (PubMed:10319817, PubMed:11136973, PubMed:10881191, PubMed:11953757, PubMed:23362938, PubMed:25824639); binds 2 tRNA(Thr) per homodimer, each tRNA contacts both monomers and makes specific contacts with the anticodon and acceptor stems (PubMed:10319817).6 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    rplAP0A7L03EBI-551254,EBI-543771

    Protein-protein interaction databases

    BioGridi4262193. 16 interactors.
    850582. 1 interactor.
    DIPiDIP-35823N.
    IntActiP0A8M3. 50 interactors.
    MINTiMINT-1229097.
    STRINGi316385.ECDH10B_1855.

    Structurei

    Secondary structure

    1642
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 5Combined sources3
    Beta strandi11 – 13Combined sources3
    Helixi20 – 27Combined sources8
    Helixi29 – 34Combined sources6
    Beta strandi37 – 40Combined sources4
    Beta strandi43 – 46Combined sources4
    Beta strandi55 – 60Combined sources6
    Helixi65 – 86Combined sources22
    Beta strandi101 – 107Combined sources7
    Helixi114 – 128Combined sources15
    Beta strandi135 – 138Combined sources4
    Helixi141 – 150Combined sources10
    Helixi154 – 163Combined sources10
    Beta strandi171 – 175Combined sources5
    Beta strandi178 – 183Combined sources6
    Helixi190 – 192Combined sources3
    Beta strandi196 – 205Combined sources10
    Helixi206 – 208Combined sources3
    Beta strandi214 – 222Combined sources9
    Helixi226 – 240Combined sources15
    Helixi244 – 250Combined sources7
    Helixi268 – 287Combined sources20
    Beta strandi297 – 300Combined sources4
    Helixi301 – 306Combined sources6
    Helixi309 – 312Combined sources4
    Helixi314 – 316Combined sources3
    Beta strandi319 – 322Combined sources4
    Beta strandi325 – 329Combined sources5
    Beta strandi331 – 333Combined sources3
    Helixi334 – 341Combined sources8
    Helixi348 – 350Combined sources3
    Beta strandi352 – 362Combined sources11
    Helixi367 – 369Combined sources3
    Turni372 – 374Combined sources3
    Beta strandi377 – 388Combined sources12
    Helixi390 – 392Combined sources3
    Helixi393 – 409Combined sources17
    Turni410 – 412Combined sources3
    Beta strandi417 – 421Combined sources5
    Helixi431 – 447Combined sources17
    Beta strandi453 – 455Combined sources3
    Beta strandi461 – 463Combined sources3
    Beta strandi465 – 471Combined sources7
    Beta strandi477 – 488Combined sources12
    Helixi489 – 492Combined sources4
    Beta strandi502 – 505Combined sources4
    Beta strandi508 – 517Combined sources10
    Helixi518 – 529Combined sources12
    Turni535 – 537Combined sources3
    Beta strandi542 – 548Combined sources7
    Helixi549 – 551Combined sources3
    Helixi552 – 564Combined sources13
    Beta strandi569 – 572Combined sources4
    Beta strandi574 – 576Combined sources3
    Helixi578 – 587Combined sources10
    Beta strandi591 – 596Combined sources6
    Helixi598 – 603Combined sources6
    Beta strandi605 – 610Combined sources6
    Beta strandi615 – 620Combined sources6
    Helixi621 – 633Combined sources13

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1EVKX-ray2.00A/B242-642[»]
    1EVLX-ray1.55A/B/C/D242-642[»]
    1FYFX-ray1.65A/B242-642[»]
    1KOGX-ray3.50A/B/C/D/E/F/G/H242-642[»]
    1QF6X-ray2.90A1-642[»]
    1TJEX-ray1.50A1-224[»]
    1TKEX-ray1.46A1-224[»]
    1TKGX-ray1.50A1-224[»]
    1TKYX-ray1.48A1-224[»]
    4HWOX-ray1.91A/B242-642[»]
    4HWPX-ray1.81A/B242-642[»]
    4HWRX-ray1.90A/B242-642[»]
    4HWSX-ray1.70A/B242-642[»]
    4P3OX-ray2.50A/B242-642[»]
    4P3PX-ray2.10A/B242-642[»]
    ProteinModelPortaliP0A8M3.
    SMRiP0A8M3.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A8M3.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni1 – 224Correctly edits mischarged seryl-tRNA(Thr)1 PublicationAdd BLAST224
    Regioni1 – 62N1 domain1 PublicationAdd BLAST62
    Regioni2 – 241N-terminal region which includes the editing domain, important for catalytic efficiency, its loss increases mischarging with L-serine, deacylation of incorrectly charged tRNA no longer occurs, partially complements a deletion strain1 PublicationAdd BLAST240
    Regioni63 – 224N2 domain, the editing domain1 PublicationAdd BLAST162
    Regioni200 – 219Contacts tRNA acceptor stem1 PublicationAdd BLAST20
    Regioni243 – 534CatalyticUniRule annotation1 PublicationAdd BLAST292
    Regioni246 – 249Contacts mRNA operator1 Publication4
    Regioni313 – 317Contacts 3'-CCA of tRNA1 Publication5
    Regioni342 – 349Contacts mRNA operator1 Publication8
    Regioni348 – 349Cross-subunit contacts with tRNA(Thr)1 Publication2
    Regioni489 – 503Contacts mRNA operator1 PublicationAdd BLAST15
    Regioni535 – 642Anticodon recognition1 PublicationAdd BLAST108
    Regioni547 – 549Contacts anticodon region of tRNA1 Publication3
    Regioni547 – 549Contacts mRNA operator1 Publication3
    Regioni575 – 586Contacts mRNA operator1 PublicationAdd BLAST12
    Regioni575 – 583Contacts anticodon region of tRNA1 Publication9
    Regioni595 – 600Contacts anticodon region of tRNA1 Publication6
    Regioni595 – 600Contacts mRNA operator1 Publication6

    Domaini

    The protein structure shows 2 N-terminal domains, the central catalytic and C-terminal domain (PubMed:10319817). The C-terminal domain recognizes the anticodon region of the tRNA while the acceptor arm is sandwiched between the N-terminal domains and the catalytic domain (PubMed:10319817). The N-terminal also contributes to the precise recognition of tRNA(Thr) (PubMed:10319817). The editing domain encompasses approximately residues 62-224; when it is removed the protein mischarges tRNA(Thr) with L-serine (PubMed:15079065, PubMed:11136973).2 Publications2 Publications

    Sequence similaritiesi

    Belongs to the class-II aminoacyl-tRNA synthetase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105C22. Bacteria.
    COG0441. LUCA.
    HOGENOMiHOG000003880.
    InParanoidiP0A8M3.
    KOiK01868.
    PhylomeDBiP0A8M3.

    Family and domain databases

    CDDicd00771. ThrRS_core. 1 hit.
    Gene3Di3.10.20.30. 1 hit.
    3.40.50.800. 1 hit.
    HAMAPiMF_00184. Thr_tRNA_synth. 1 hit.
    InterProiView protein in InterPro
    IPR002314. aa-tRNA-synt_IIb.
    IPR006195. aa-tRNA-synth_II.
    IPR004154. Anticodon-bd.
    IPR036621. Anticodon-bd_dom_sf.
    IPR012675. Beta-grasp_dom_sf.
    IPR004095. TGS.
    IPR012676. TGS-like.
    IPR002320. Thr-tRNA-ligase_IIa.
    IPR018163. Thr/Ala-tRNA-synth_IIc_edit.
    IPR033728. ThrRS_core.
    IPR012947. tRNA_SAD.
    PANTHERiPTHR11451. PTHR11451. 1 hit.
    PfamiView protein in Pfam
    PF03129. HGTP_anticodon. 1 hit.
    PF02824. TGS. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    PF07973. tRNA_SAD. 1 hit.
    PRINTSiPR01047. TRNASYNTHTHR.
    SMARTiView protein in SMART
    SM00863. tRNA_SAD. 1 hit.
    SUPFAMiSSF52954. SSF52954. 1 hit.
    SSF55186. SSF55186. 1 hit.
    SSF81271. SSF81271. 1 hit.
    TIGRFAMsiTIGR00418. thrS. 1 hit.
    PROSITEiView protein in PROSITE
    PS50862. AA_TRNA_LIGASE_II. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0A8M3-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MPVITLPDGS QRHYDHAVSP MDVALDIGPG LAKACIAGRV NGELVDACDL
    60 70 80 90 100
    IENDAQLSII TAKDEEGLEI IRHSCAHLLG HAIKQLWPHT KMAIGPVIDN
    110 120 130 140 150
    GFYYDVDLDR TLTQEDVEAL EKRMHELAEK NYDVIKKKVS WHEARETFAN
    160 170 180 190 200
    RGESYKVSIL DENIAHDDKP GLYFHEEYVD MCRGPHVPNM RFCHHFKLMK
    210 220 230 240 250
    TAGAYWRGDS NNKMLQRIYG TAWADKKALN AYLQRLEEAA KRDHRKIGKQ
    260 270 280 290 300
    LDLYHMQEEA PGMVFWHNDG WTIFRELEVF VRSKLKEYQY QEVKGPFMMD
    310 320 330 340 350
    RVLWEKTGHW DNYKDAMFTT SSENREYCIK PMNCPGHVQI FNQGLKSYRD
    360 370 380 390 400
    LPLRMAEFGS CHRNEPSGSL HGLMRVRGFT QDDAHIFCTE EQIRDEVNGC
    410 420 430 440 450
    IRLVYDMYST FGFEKIVVKL STRPEKRIGS DEMWDRAEAD LAVALEENNI
    460 470 480 490 500
    PFEYQLGEGA FYGPKIEFTL YDCLDRAWQC GTVQLDFSLP SRLSASYVGE
    510 520 530 540 550
    DNERKVPVMI HRAILGSMER FIGILTEEFA GFFPTWLAPV QVVIMNITDS
    560 570 580 590 600
    QSEYVNELTQ KLSNAGIRVK ADLRNEKIGF KIREHTLRRV PYMLVCGDKE
    610 620 630 640
    VESGKVAVRT RRGKDLGSMD VNEVIEKLQQ EIRSRSLKQL EE
    Length:642
    Mass (Da):74,014
    Last modified:June 7, 2005 - v1
    Checksum:i38D8913B19CDAB7B
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti195H → R in CAA23560 (PubMed:6353409).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    V00291 Genomic DNA. Translation: CAA23560.1.
    U00096 Genomic DNA. Translation: AAC74789.1.
    AP009048 Genomic DNA. Translation: BAA15498.1.
    M13549 Genomic DNA. Translation: AAA24674.1.
    PIRiG64930. SYECTT.
    RefSeqiNP_416234.1. NC_000913.3.
    WP_001144202.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74789; AAC74789; b1719.
    BAA15498; BAA15498; BAA15498.
    GeneIDi946222.
    KEGGiecj:JW1709.
    eco:b1719.
    PATRICifig|1411691.4.peg.538.

    Similar proteinsi

    Entry informationi

    Entry nameiSYT_ECOLI
    AccessioniPrimary (citable) accession number: P0A8M3
    Secondary accession number(s): P00955, P78166, P78241
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: June 7, 2005
    Last modified: November 22, 2017
    This is version 119 of the entry and version 1 of the sequence. See 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families