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Q9XDB4

- SYI_FERPD

UniProt

Q9XDB4 - SYI_FERPD

Protein

Isoleucine--tRNA ligase

Gene

ileS

Organism
Fervidobacterium pennivorans (strain DSM 9078 / Ven5)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 86 (01 Oct 2014)
      Sequence version 3 (05 Sep 2012)
      Previous versions | rss
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    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).UniRule annotation

    Catalytic activityi

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

    Cofactori

    Binds 1 zinc ion per subunit.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei549 – 5491Aminoacyl-adenylateUniRule annotation
    Binding sitei593 – 5931ATPUniRule annotation
    Metal bindingi880 – 8801ZincUniRule annotation
    Metal bindingi883 – 8831ZincUniRule annotation
    Metal bindingi900 – 9001ZincUniRule annotation
    Metal bindingi903 – 9031ZincUniRule annotation

    GO - Molecular functioni

    1. aminoacyl-tRNA editing activity Source: InterPro
    2. ATP binding Source: UniProtKB-HAMAP
    3. isoleucine-tRNA ligase activity Source: UniProtKB-HAMAP
    4. zinc ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. isoleucyl-tRNA aminoacylation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciFPEN771875:GLDA-1791-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isoleucine--tRNA ligaseUniRule annotation (EC:6.1.1.5UniRule annotation)
    Alternative name(s):
    Isoleucyl-tRNA synthetaseUniRule annotation
    Short name:
    IleRSUniRule annotation
    Gene namesi
    Name:ileSUniRule annotation
    Ordered Locus Names:Ferpe_1791
    OrganismiFervidobacterium pennivorans (strain DSM 9078 / Ven5)
    Taxonomic identifieri771875 [NCBI]
    Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeFervidobacterium
    ProteomesiUP000007384: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 912912Isoleucine--tRNA ligasePRO_0000098387Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi57 – 6711"HIGH" regionAdd
    BLAST
    Motifi590 – 5945"KMSKS" region

    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)).UniRule annotation

    Sequence similaritiesi

    Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily.UniRule annotation

    Phylogenomic databases

    KOiK01870.

    Family and domain databases

    Gene3Di1.10.730.10. 1 hit.
    3.40.50.620. 2 hits.
    3.90.740.10. 1 hit.
    HAMAPiMF_02002. Ile_tRNA_synth_type1.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002300. aa-tRNA-synth_Ia.
    IPR002301. Ile-tRNA-ligase.
    IPR023585. Ile-tRNA-ligase_type1.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR009080. tRNAsynth_1a_anticodon-bd.
    IPR013155. V/L/I-tRNA-synth_anticodon-bd.
    IPR009008. Val/Leu/Ile-tRNA-synth_edit.
    IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
    [Graphical view]
    PANTHERiPTHR11946:SF9. PTHR11946:SF9. 1 hit.
    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.

    Q9XDB4-1 [UniParc]FASTAAdd to Basket

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    MDYKATLNLP QTNFQMKANL VNKEPEMLKF WEEKEIYKKT LETRANAPTY    50
    LLHDGPPYAN GDIHLGTAMN KILKDFVTRY KTMRGYRVPF VPGWDTHGLP 100
    IEHRVTTSLG EEAKKKSPAE IRKLCKEFAL KYVDIQREEF KRLGVKGDWE 150
    HPYITLDPDY EYHILDVFKT LVENGNVYRG NKPVYWCPTC RTALAEAEIE 200
    YHDHESPSIY VKFQMVDKPD TYIVIWTTTP WTIPANVAIA LHPDYTYVKI 250
    KVDEEYWIVA EGLLQKFAAD VGIDFEVVEK FVGKELEGKL TKHPLYDRTS 300
    VVVLADYVTL EDGTGCVHTA PGHGEEDYQT GLKYNLPVLS PVDDEGRFTK 350
    EAGKYEGLKI WDANKVIVED LKNNGSLIKA GKISHSYPHC WRCKGPVMFR 400
    ATPQWFISVD KNNLRGKVLE EIKKVKWYPA WGETRITAMV QERPDWTISR 450
    QRVWGVPIPA VKCKDCGEVT LEPKVIEHFA NIVKEKGTDA WFELDVNELI 500
    PADFKCPACG SKNFEKTHDT LDVWIDSGCS WEAVIRSKGE RFPVDLYLEG 550
    DDQHRGWFQS SIFLSTAKAG TAPFKAVVTH GFIKDEQGRK MSKSLGNVID 600
    PMEIVNKYGA DILRLWVAST DFFDNIRVGK NIIEQQVEVY RKLRNTLRYL 650
    LSNLYDFTEA DLLPYEKLLP LDKWALGRLQ KFIEQITQYY EGFEYSKVYN 700
    ATVKYCTTEL SAVYLDILKD RLYVEAKDSI YRRSAQTALH YILEALIKIL 750
    APIIPFTAEE AYQESHLKRY ESVHLEYWPE VRKEFIDEAL LEEFDHLLLI 800
    RDDVLKALEN ARASDIIGHS LDAHVIIEAK NEELKNLLRK YESLLEEFFI 850
    VSKVTLSENI SGLNGQFANV LVQRAEGQKC QRCWKYHPDT GKDLEHPETC 900
    PRCSAVLRGE RK 912
    Length:912
    Mass (Da):105,259
    Last modified:September 5, 2012 - v3
    Checksum:iA0C8FA7C5CE20B7E
    GO

    Sequence cautioni

    The sequence AAD30388.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti525 – 5251I → M in AAD30388. (PubMed:10224005)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF096862 Genomic DNA. Translation: AAD30388.1. Different initiation.
    CP003260 Genomic DNA. Translation: AFG35844.1.
    RefSeqiYP_005471963.1. NC_017095.1.

    Genome annotation databases

    EnsemblBacteriaiAFG35844; AFG35844; Ferpe_1791.
    GeneIDi12058543.
    KEGGifpe:Ferpe_1791.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF096862 Genomic DNA. Translation: AAD30388.1 . Different initiation.
    CP003260 Genomic DNA. Translation: AFG35844.1 .
    RefSeqi YP_005471963.1. NC_017095.1.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AFG35844 ; AFG35844 ; Ferpe_1791 .
    GeneIDi 12058543.
    KEGGi fpe:Ferpe_1791.

    Phylogenomic databases

    KOi K01870.

    Enzyme and pathway databases

    BioCyci FPEN771875:GLDA-1791-MONOMER.

    Family and domain databases

    Gene3Di 1.10.730.10. 1 hit.
    3.40.50.620. 2 hits.
    3.90.740.10. 1 hit.
    HAMAPi MF_02002. Ile_tRNA_synth_type1.
    InterProi IPR001412. aa-tRNA-synth_I_CS.
    IPR002300. aa-tRNA-synth_Ia.
    IPR002301. Ile-tRNA-ligase.
    IPR023585. Ile-tRNA-ligase_type1.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR009080. tRNAsynth_1a_anticodon-bd.
    IPR013155. V/L/I-tRNA-synth_anticodon-bd.
    IPR009008. Val/Leu/Ile-tRNA-synth_edit.
    IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
    [Graphical view ]
    PANTHERi PTHR11946:SF9. PTHR11946:SF9. 1 hit.
    Pfami PF08264. Anticodon_1. 1 hit.
    PF00133. tRNA-synt_1. 1 hit.
    PF06827. zf-FPG_IleRS. 1 hit.
    [Graphical view ]
    PRINTSi PR00984. TRNASYNTHILE.
    SUPFAMi SSF47323. SSF47323. 1 hit.
    SSF50677. SSF50677. 1 hit.
    TIGRFAMsi TIGR00392. ileS. 1 hit.
    PROSITEi PS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Pullulanase type I from fervidobacterium pennavorans ven5: cloning, sequencing, and expression of the gene and biochemical characterization of the recombinant enzyme."
      Bertoldo C., Duffner F., Jorgensen P.L., Antranikian G.
      Appl. Environ. Microbiol. 65:2084-2091(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: DSM 9078 / Ven5.
    2. "Complete sequence of Fervidobacterium pennivorans DSM 9078."
      Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Ovchinnikova G., Lu M., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Pagani I., Noll K.M., Woyke T.
      Submitted (MAR-2012) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: DSM 9078 / Ven5.

    Entry informationi

    Entry nameiSYI_FERPD
    AccessioniPrimary (citable) accession number: Q9XDB4
    Secondary accession number(s): H9UEA1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: September 5, 2012
    Last modified: October 1, 2014
    This is version 86 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3