ID   SYI_NITWN               Reviewed;         999 AA.
AC   Q3SPJ6;
DT   20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   11-OCT-2005, sequence version 1.
DT   03-AUG-2022, entry version 115.
DE   RecName: Full=Isoleucine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_02002};
DE            EC=6.1.1.5 {ECO:0000255|HAMAP-Rule:MF_02002};
DE   AltName: Full=Isoleucyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_02002};
DE            Short=IleRS {ECO:0000255|HAMAP-Rule:MF_02002};
GN   Name=ileS {ECO:0000255|HAMAP-Rule:MF_02002}; OrderedLocusNames=Nwi_2542;
OS   Nitrobacter winogradskyi (strain ATCC 25391 / DSM 10237 / CIP 104748 /
OS   NCIMB 11846 / Nb-255).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Bradyrhizobiaceae; Nitrobacter.
OX   NCBI_TaxID=323098;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25391 / DSM 10237 / CIP 104748 / NCIMB 11846 / Nb-255;
RX   PubMed=16517654; DOI=10.1128/aem.72.3.2050-2063.2006;
RA   Starkenburg S.R., Chain P.S.G., Sayavedra-Soto L.A., Hauser L., Land M.L.,
RA   Larimer F.W., Malfatti S.A., Klotz M.G., Bottomley P.J., Arp D.J.,
RA   Hickey W.J.;
RT   "Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium
RT   Nitrobacter winogradskyi Nb-255.";
RL   Appl. Environ. Microbiol. 72:2050-2063(2006).
CC   -!- FUNCTION: Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS
CC       can inadvertently accommodate and process structurally similar amino
CC       acids such as valine, to avoid such errors it has two additional
CC       distinct tRNA(Ile)-dependent editing activities. One activity is
CC       designated as 'pretransfer' editing and involves the hydrolysis of
CC       activated Val-AMP. The other activity is designated 'posttransfer'
CC       editing and involves deacylation of mischarged Val-tRNA(Ile).
CC       {ECO:0000255|HAMAP-Rule:MF_02002}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-
CC         isoleucyl-tRNA(Ile); Xref=Rhea:RHEA:11060, Rhea:RHEA-COMP:9666,
CC         Rhea:RHEA-COMP:9695, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC         ChEBI:CHEBI:58045, ChEBI:CHEBI:78442, ChEBI:CHEBI:78528,
CC         ChEBI:CHEBI:456215; EC=6.1.1.5; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_02002};
CC   -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_02002}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_02002}.
CC   -!- DOMAIN: IleRS has two distinct active sites: one for aminoacylation and
CC       one for editing. The misactivated valine is translocated from the
CC       active site to the editing site, which sterically excludes the
CC       correctly activated isoleucine. The single editing site contains two
CC       valyl binding pockets, one specific for each substrate (Val-AMP or Val-
CC       tRNA(Ile)). {ECO:0000255|HAMAP-Rule:MF_02002}.
CC   -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC       IleS type 1 subfamily. {ECO:0000255|HAMAP-Rule:MF_02002}.
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DR   EMBL; CP000115; ABA05795.1; -; Genomic_DNA.
DR   RefSeq; WP_011315746.1; NC_007406.1.
DR   AlphaFoldDB; Q3SPJ6; -.
DR   SMR; Q3SPJ6; -.
DR   STRING; 323098.Nwi_2542; -.
DR   PRIDE; Q3SPJ6; -.
DR   EnsemblBacteria; ABA05795; ABA05795; Nwi_2542.
DR   KEGG; nwi:Nwi_2542; -.
DR   eggNOG; COG0060; Bacteria.
DR   HOGENOM; CLU_001493_7_1_5; -.
DR   OMA; HLGTAWN; -.
DR   OrthoDB; 32262at2; -.
DR   Proteomes; UP000002531; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0002161; F:aminoacyl-tRNA editing activity; IEA:InterPro.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0004822; F:isoleucine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0000049; F:tRNA binding; IEA:InterPro.
DR   GO; GO:0006428; P:isoleucyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR   CDD; cd07960; Anticodon_Ia_Ile_BEm; 1.
DR   Gene3D; 3.40.50.620; -; 2.
DR   Gene3D; 3.90.740.10; -; 1.
DR   HAMAP; MF_02002; Ile_tRNA_synth_type1; 1.
DR   InterPro; IPR001412; aa-tRNA-synth_I_CS.
DR   InterPro; IPR002300; aa-tRNA-synth_Ia.
DR   InterPro; IPR033708; Anticodon_Ile_BEm.
DR   InterPro; IPR002301; Ile-tRNA-ligase.
DR   InterPro; IPR023585; Ile-tRNA-ligase_type1.
DR   InterPro; IPR013155; M/V/L/I-tRNA-synth_anticd-bd.
DR   InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR   InterPro; IPR009080; tRNAsynth_Ia_anticodon-bd.
DR   InterPro; IPR009008; Val/Leu/Ile-tRNA-synth_edit.
DR   Pfam; PF08264; Anticodon_1; 1.
DR   Pfam; PF00133; tRNA-synt_1; 1.
DR   PRINTS; PR00984; TRNASYNTHILE.
DR   SUPFAM; SSF47323; SSF47323; 1.
DR   SUPFAM; SSF50677; SSF50677; 1.
DR   TIGRFAMs; TIGR00392; ileS; 1.
DR   PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
PE   3: Inferred from homology;
KW   Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW   Nucleotide-binding; Protein biosynthesis; Reference proteome.
FT   CHAIN           1..999
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_0000098430"
FT   MOTIF           67..77
FT                   /note="'HIGH' region"
FT   MOTIF           668..672
FT                   /note="'KMSKS' region"
FT   BINDING         627
FT                   /ligand="L-isoleucyl-5'-AMP"
FT                   /ligand_id="ChEBI:CHEBI:178002"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         671
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
SQ   SEQUENCE   999 AA;  111640 MW;  689891A0DB8D55C8 CRC64;
     MTEKKKNSDA PDYAKTLFLP QTEFPMRAGL PQREPDILKR WTDIDLYGQL RACAKGRPKF
     VLHDGPPYAN GSIHIGHALN KILKDVVTKS QQMLGHDSNY VPGWDCHGLP IEWKIEEENY
     RSKGKTKPNF KDPAAMVAFR KECRAYAEHW LNVQREQFKR LGIIGDWDHP YATMTYPAEA
     QIARELMKFA ANGTLYRGSK PVMWSVVEKT ALAEAEVEYE DHTSDTVWVK FPVTSPAHGA
     LSQASVVIWT TTPWTLPGNR AISFSNKIAY GLYKITDAPA DNWAKTGDVL ILANKLAGEV
     FKQARVTAYE KVRDIPADTL DAVECAHPLK GLSGGYEFTV PLLDGDHVTD DTGTGFVHTA
     PGHGREDFDI WTANARELEV RGISSTIPYT VDENGALTAQ APGFEGKRVI DDKGNKGDAN
     EAVIKALVER NRLLARGRLK HQYPHSWRSK KPVIFRNTPQ WFIAMDRDIA DDGKANHGDT
     LRARALQAIS VTRWVPPAGQ NRITGMIANR PDWVISRQRA WGVPIAVFVR EKGDGSAEVL
     IDDAVNRRIS DAFEKEGADA WYAEGARERF LGDRAGEDWS KVDDILDVWF DSGSTHAFVL
     EDPAHFPSLR DIKRKADGGR DTVMYLEGSD QHRGWFHSSL LESCGTRGRA PYDIVLTHGF
     TLDENGRKMS KSLGNTVDPQ KVIKDSGADI LRLWVCATDY ADDQRIGPEI LKNTIETYRK
     LRNTIRWMLG TLHHFDRGEA VAFTEMPELE RLMLHRLAEQ SALVRSAYAE FDYKTVVASL
     AAFMNTELSA FYFDIRKDTL YCDPPSSPAR KAALTVIDKL CDAILKWLAP VLSFTTEEAW
     RLYRPDAEPS VHLTLFPESF DNFRDDSLAA KWETVRAVRS VVTGALELER AAKRIGSSLE
     ASPIVHVADR AMLGTLFDID LAEVCITSNF EVREGDAPDG AFRLPNVQGV AVVVEKAAGT
     KCARSWKILP TVGSDSEYPD VSPRDAQALR EWKALGVTV