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Protein

Isoleucine--tRNA ligase

Gene

ileS

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 isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile).

Catalytic activityi

ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile).

Cofactori

Zn2+Note: Binds 1 zinc ion per subunit.

Kineticsi

  1. KM=5 µM for isoleucine1 Publication
  2. KM=0.4 mM for ATP1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei561Aminoacyl-adenylateBy similarity1
    Binding sitei605ATPBy similarity1
    Metal bindingi901ZincBy similarity1
    Metal bindingi904ZincBy similarity1
    Metal bindingi921ZincBy similarity1
    Metal bindingi924ZincBy similarity1

    GO - Molecular functioni

    • aminoacyl-tRNA editing activity Source: InterPro
    • ATP binding Source: UniProtKB-HAMAP
    • isoleucine-tRNA ligase activity Source: GO_Central
    • tRNA binding Source: InterPro
    • zinc ion binding Source: EcoCyc

    GO - Biological processi

    • isoleucyl-tRNA aminoacylation Source: EcoCyc
    • response to antibiotic Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Antibiotic resistance, Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:ILES-MONOMER.
    ECOL316407:JW0024-MONOMER.
    MetaCyc:ILES-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isoleucine--tRNA ligase (EC:6.1.1.5)
    Alternative name(s):
    Isoleucyl-tRNA synthetase
    Short name:
    IleRS
    Gene namesi
    Name:ileS
    Synonyms:ilvS
    Ordered Locus Names:b0026, JW0024
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10492. ileS.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi94G → R: 6000-fold increase in Km for isoleucine and 4-fold increase in Km for ATP, with no effect on activity. 1 Publication1
    Mutagenesisi97C → S: No effect on activity. 1 Publication1
    Mutagenesisi102I → N: No significant effect on activity. 1 Publication1
    Mutagenesisi183K → A: Abolishes translocation from the aminoacylation site to the editing site, without effect on aminoacylation activity and posttransfer editing; when associated with A-421. 1 Publication1
    Mutagenesisi241T → A: Nearly the same editing activity as the wild-type. 1 Publication1
    Mutagenesisi242T → A: Abolishes editing activity against valine, with little change in aminoacylation activity; when associated with A-250. 1 Publication1
    Mutagenesisi242T → P: Abolishes editing activity against valine, with little change in aminoacylation activity. 1 Publication1
    Mutagenesisi243T → A: Abolishes editing activity against valine, with little change in aminoacylation activity. 2 Publications1
    Mutagenesisi243T → R: Abolishes pretransfer editing. 2 Publications1
    Mutagenesisi246T → A: Nearly the same editing activity as the wild-type. 1 Publication1
    Mutagenesisi250N → A: Abolishes editing activity against valine, with little change in aminoacylation activity. 2 Publications1
    Mutagenesisi333H → A: Alters the specificity for hydrolysis of the aminoacyl tRNA ester, with no effect on pretransfer editing. 1 Publication1
    Mutagenesisi342D → A or N: Strong decrease in total editing and deacylation activities. Severely deficient in translocation from the aminoacylation site to the editing site. 1 Publication1
    Mutagenesisi342D → E: Reduces 2- to 3-fold the total editing activity and 2-fold the deacylation activity. Moderately reduces translocation from the aminoacylation site to the editing site. 1 Publication1
    Mutagenesisi421W → A: Abolishes translocation from the aminoacylation site to the editing site, without effect on aminoacylation activity and posttransfer editing; when associated with A-183. 1 Publication1

    Chemistry databases

    ChEMBLiCHEMBL3657.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00000983842 – 938Isoleucine--tRNA ligaseAdd BLAST937

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei183N6-acetyllysine1 Publication1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    EPDiP00956.
    PaxDbiP00956.
    PRIDEiP00956.

    Interactioni

    Subunit structurei

    Monomer.

    Protein-protein interaction databases

    BioGridi849163. 1 interactor.
    DIPiDIP-10017N.
    IntActiP00956. 16 interactors.
    MINTiMINT-1232480.
    STRINGi511145.b0026.

    Chemistry databases

    BindingDBiP00956.

    Structurei

    3D structure databases

    ProteinModelPortaliP00956.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi58 – 68"HIGH" regionAdd BLAST11
    Motifi602 – 606"KMSKS" region5

    Domaini

    IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)).

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C07. Bacteria.
    COG0060. LUCA.
    HOGENOMiHOG000246402.
    InParanoidiP00956.
    KOiK01870.
    OMAiPIPFFLH.
    PhylomeDBiP00956.

    Family and domain databases

    CDDicd07960. Anticodon_Ia_Ile_BEm. 1 hit.
    Gene3Di1.10.730.10. 1 hit.
    3.40.50.620. 2 hits.
    3.90.740.10. 1 hit.
    HAMAPiMF_02002. Ile_tRNA_synth_type1. 1 hit.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002300. aa-tRNA-synth_Ia.
    IPR033708. Anticodon_Ile_BEm.
    IPR002301. Ile-tRNA-ligase.
    IPR023585. Ile-tRNA-ligase_type1.
    IPR013155. M/V/L/I-tRNA-synth_anticd-bd.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR009080. tRNAsynth_Ia_anticodon-bd.
    IPR009008. Val/Leu/Ile-tRNA-synth_edit.
    IPR010663. Znf_FPG/IleRS.
    [Graphical view]
    PfamiPF08264. Anticodon_1. 1 hit.
    PF00133. tRNA-synt_1. 1 hit.
    PF06827. zf-FPG_IleRS. 1 hit.
    [Graphical view]
    PRINTSiPR00984. TRNASYNTHILE.
    SUPFAMiSSF47323. SSF47323. 1 hit.
    SSF50677. SSF50677. 1 hit.
    TIGRFAMsiTIGR00392. ileS. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P00956-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSDYKSTLNL PETGFPMRGD LAKREPGMLA RWTDDDLYGI IRAAKKGKKT
    60 70 80 90 100
    FILHDGPPYA NGSIHIGHSV NKILKDIIVK SKGLSGYDSP YVPGWDCHGL
    110 120 130 140 150
    PIELKVEQEY GKPGEKFTAA EFRAKCREYA ATQVDGQRKD FIRLGVLGDW
    160 170 180 190 200
    SHPYLTMDFK TEANIIRALG KIIGNGHLHK GAKPVHWCVD CRSALAEAEV
    210 220 230 240 250
    EYYDKTSPSI DVAFQAVDQD ALKAKFAVSN VNGPISLVIW TTTPWTLPAN
    260 270 280 290 300
    RAISIAPDFD YALVQIDGQA VILAKDLVES VMQRIGVTDY TILGTVKGAE
    310 320 330 340 350
    LELLRFTHPF MGFDVPAILG DHVTLDAGTG AVHTAPGHGP DDYVIGQKYG
    360 370 380 390 400
    LETANPVGPD GTYLPGTYPT LDGVNVFKAN DIVVALLQEK GALLHVEKMQ
    410 420 430 440 450
    HSYPCCWRHK TPIIFRATPQ WFVSMDQKGL RAQSLKEIKG VQWIPDWGQA
    460 470 480 490 500
    RIESMVANRP DWCISRQRTW GVPMSLFVHK DTEELHPRTL ELMEEVAKRV
    510 520 530 540 550
    EVDGIQAWWD LDAKEILGDE ADQYVKVPDT LDVWFDSGST HSSVVDVRPE
    560 570 580 590 600
    FAGHAADMYL EGSDQHRGWF MSSLMISTAM KGKAPYRQVL THGFTVDGQG
    610 620 630 640 650
    RKMSKSIGNT VSPQDVMNKL GADILRLWVA STDYTGEMAV SDEILKRAAD
    660 670 680 690 700
    SYRRIRNTAR FLLANLNGFD PAKDMVKPEE MVVLDRWAVG CAKAAQEDIL
    710 720 730 740 750
    KAYEAYDFHE VVQRLMRFCS VEMGSFYLDI IKDRQYTAKA DSVARRSCQT
    760 770 780 790 800
    ALYHIAEALV RWMAPILSFT ADEVWGYLPG EREKYVFTGE WYEGLFGLAD
    810 820 830 840 850
    SEAMNDAFWD ELLKVRGEVN KVIEQARADK KVGGSLEAAV TLYAEPELSA
    860 870 880 890 900
    KLTALGDELR FVLLTSGATV ADYNDAPADA QQSEVLKGLK VALSKAEGEK
    910 920 930
    CPRCWHYTQD VGKVAEHAEI CGRCVSNVAG DGEKRKFA
    Length:938
    Mass (Da):104,297
    Last modified:January 23, 2007 - v5
    Checksum:i238CEDAF461F01D5
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti243 – 264TPWTL…DYALV → RRGLCLPTAQSLLHQISTMR WW AA sequence (PubMed:6390679).CuratedAdd BLAST22
    Sequence conflicti300 – 301EL → DV AA sequence (PubMed:6390679).Curated2
    Sequence conflicti587R → C AA sequence (PubMed:6390679).Curated1
    Sequence conflicti637E → Q AA sequence (PubMed:6390679).Curated1
    Sequence conflicti724G → V AA sequence (PubMed:6390679).Curated1
    Sequence conflicti738A → P AA sequence (PubMed:6390679).Curated1
    Sequence conflicti740 – 743ADSV → RTVW AA sequence (PubMed:6390679).Curated4
    Sequence conflicti787F → L AA sequence (PubMed:6390679).Curated1
    Sequence conflicti830K → N AA sequence (PubMed:6390679).Curated1
    Sequence conflicti867 – 869GAT → DRRY AA sequence (PubMed:6390679).Curated3

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural varianti594F → L in strain: PS102. 1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC73137.1.
    AP009048 Genomic DNA. Translation: BAB96595.2.
    M10428 Genomic DNA. Translation: AAA24606.1.
    X00776 Genomic DNA. Translation: CAA25352.1.
    K01990 Genomic DNA. Translation: AAA24091.1.
    PIRiB64723. SYECIT.
    RefSeqiNP_414567.1. NC_000913.3.
    WP_001286857.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73137; AAC73137; b0026.
    BAB96595; BAB96595; BAB96595.
    GeneIDi944761.
    KEGGiecj:JW0024.
    eco:b0026.
    PATRICi32115143. VBIEscCol129921_0023.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC73137.1.
    AP009048 Genomic DNA. Translation: BAB96595.2.
    M10428 Genomic DNA. Translation: AAA24606.1.
    X00776 Genomic DNA. Translation: CAA25352.1.
    K01990 Genomic DNA. Translation: AAA24091.1.
    PIRiB64723. SYECIT.
    RefSeqiNP_414567.1. NC_000913.3.
    WP_001286857.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP00956.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi849163. 1 interactor.
    DIPiDIP-10017N.
    IntActiP00956. 16 interactors.
    MINTiMINT-1232480.
    STRINGi511145.b0026.

    Chemistry databases

    BindingDBiP00956.
    ChEMBLiCHEMBL3657.

    Proteomic databases

    EPDiP00956.
    PaxDbiP00956.
    PRIDEiP00956.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73137; AAC73137; b0026.
    BAB96595; BAB96595; BAB96595.
    GeneIDi944761.
    KEGGiecj:JW0024.
    eco:b0026.
    PATRICi32115143. VBIEscCol129921_0023.

    Organism-specific databases

    EchoBASEiEB0487.
    EcoGeneiEG10492. ileS.

    Phylogenomic databases

    eggNOGiENOG4105C07. Bacteria.
    COG0060. LUCA.
    HOGENOMiHOG000246402.
    InParanoidiP00956.
    KOiK01870.
    OMAiPIPFFLH.
    PhylomeDBiP00956.

    Enzyme and pathway databases

    BioCyciEcoCyc:ILES-MONOMER.
    ECOL316407:JW0024-MONOMER.
    MetaCyc:ILES-MONOMER.

    Miscellaneous databases

    PROiP00956.

    Family and domain databases

    CDDicd07960. Anticodon_Ia_Ile_BEm. 1 hit.
    Gene3Di1.10.730.10. 1 hit.
    3.40.50.620. 2 hits.
    3.90.740.10. 1 hit.
    HAMAPiMF_02002. Ile_tRNA_synth_type1. 1 hit.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002300. aa-tRNA-synth_Ia.
    IPR033708. Anticodon_Ile_BEm.
    IPR002301. Ile-tRNA-ligase.
    IPR023585. Ile-tRNA-ligase_type1.
    IPR013155. M/V/L/I-tRNA-synth_anticd-bd.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR009080. tRNAsynth_Ia_anticodon-bd.
    IPR009008. Val/Leu/Ile-tRNA-synth_edit.
    IPR010663. Znf_FPG/IleRS.
    [Graphical view]
    PfamiPF08264. Anticodon_1. 1 hit.
    PF00133. tRNA-synt_1. 1 hit.
    PF06827. zf-FPG_IleRS. 1 hit.
    [Graphical view]
    PRINTSiPR00984. TRNASYNTHILE.
    SUPFAMiSSF47323. SSF47323. 1 hit.
    SSF50677. SSF50677. 1 hit.
    TIGRFAMsiTIGR00392. ileS. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiSYI_ECOLI
    AccessioniPrimary (citable) accession number: P00956
    Secondary accession number(s): P78038, Q59429
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: November 2, 2016
    This is version 170 of the entry and version 5 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Strain PS102 is resistant to the antibiotic mupirocin (pseudomonic acid A), an Ile-analog that competitively inhibits activation by Ile-tRNA synthetase, thus inhibiting protein biosynthesis.

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, 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. 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.