ID   SYI_LARHH               Reviewed;         957 AA.
AC   C1DCX2;
DT   22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT   26-MAY-2009, sequence version 1.
DT   18-JUN-2025, entry version 90.
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};
GN   OrderedLocusNames=LHK_00614;
OS   Laribacter hongkongensis (strain HLHK9).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Betaproteobacteria; Neisseriales;
OC   Aquaspirillaceae; Laribacter.
OX   NCBI_TaxID=557598;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=HLHK9;
RX   PubMed=19283063; DOI=10.1371/journal.pgen.1000416;
RA   Woo P.C.Y., Lau S.K.P., Tse H., Teng J.L.L., Curreem S.O., Tsang A.K.L.,
RA   Fan R.Y.Y., Wong G.K.M., Huang Y., Loman N.J., Snyder L.A.S., Cai J.J.,
RA   Huang J.-D., Mak W., Pallen M.J., Lok S., Yuen K.-Y.;
RT   "The complete genome and proteome of Laribacter hongkongensis reveal
RT   potential mechanisms for adaptations to different temperatures and
RT   habitats.";
RL   PLoS Genet. 5:E1000416-E1000416(2009).
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=tRNA(Ile) + L-isoleucine + ATP = L-isoleucyl-tRNA(Ile) + AMP +
CC         diphosphate; Xref=Rhea:RHEA:11060, Rhea:RHEA-COMP:9666, Rhea:RHEA-
CC         COMP:9695, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:58045,
CC         ChEBI:CHEBI:78442, ChEBI:CHEBI:78528, ChEBI:CHEBI:456215; EC=6.1.1.5;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_02002};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_02002};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-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; CP001154; ACO73607.1; -; Genomic_DNA.
DR   RefSeq; WP_012696099.1; NC_012559.1.
DR   AlphaFoldDB; C1DCX2; -.
DR   SMR; C1DCX2; -.
DR   STRING; 557598.LHK_00614; -.
DR   KEGG; lhk:LHK_00614; -.
DR   eggNOG; COG0060; Bacteria.
DR   HOGENOM; CLU_001493_7_1_4; -.
DR   Proteomes; UP000002010; Chromosome.
DR   GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
DR   GO; GO:0002161; F:aminoacyl-tRNA deacylase 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:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0006428; P:isoleucyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR   CDD; cd07960; Anticodon_Ia_Ile_BEm; 1.
DR   FunFam; 3.40.50.620:FF:000048; Isoleucine--tRNA ligase; 1.
DR   Gene3D; 1.10.730.20; -; 1.
DR   Gene3D; 3.40.50.620; HUPs; 2.
DR   Gene3D; 1.10.10.830; Ile-tRNA synthetase CP2 domain-like; 1.
DR   Gene3D; 3.90.740.10; Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain; 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; IPR050081; Ile-tRNA_ligase.
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   InterPro; IPR010663; Znf_FPG/IleRS.
DR   NCBIfam; TIGR00392; ileS; 1.
DR   PANTHER; PTHR42765:SF1; ISOLEUCINE--TRNA LIGASE, MITOCHONDRIAL; 1.
DR   PANTHER; PTHR42765; SOLEUCYL-TRNA SYNTHETASE; 1.
DR   Pfam; PF08264; Anticodon_1; 1.
DR   Pfam; PF00133; tRNA-synt_1; 2.
DR   Pfam; PF06827; zf-FPG_IleRS; 1.
DR   PRINTS; PR00984; TRNASYNTHILE.
DR   SUPFAM; SSF47323; Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases; 1.
DR   SUPFAM; SSF52374; Nucleotidylyl transferase; 1.
DR   SUPFAM; SSF50677; ValRS/IleRS/LeuRS editing domain; 1.
DR   PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
PE   3: Inferred from homology;
KW   Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase; Metal-binding;
KW   Nucleotide-binding; Protein biosynthesis; Reference proteome; Zinc.
FT   CHAIN           1..957
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_1000216239"
FT   MOTIF           57..67
FT                   /note="'HIGH' region"
FT   MOTIF           635..639
FT                   /note="'KMSKS' region"
FT   BINDING         594
FT                   /ligand="L-isoleucyl-5'-AMP"
FT                   /ligand_id="ChEBI:CHEBI:178002"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         638
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         920
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         923
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         940
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         943
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
SQ   SEQUENCE   957 AA;  106364 MW;  F4891ED2EA3BB86F CRC64;
     MDLKKTVNLL DTPFPMRGDL ARREPGWLAQ WQAQQRYQKL RKIAAGRPKF ILHDGPPYAN
     GDIHIGHAVN KILKDIIVRS KTQAGFDAPY VPGWDCHGLP IEHQIEKLVK GDKKAIEAAP
     SIHARITEYR KANGLDAKAT DLPASFIREL CREYAGLQVE RQKKDFIRLG VLGEWDNPYR
     TMSFRSEADE IRALGKLYQQ GYLFKGLKPV YWCFDCGSAL AEAEVEYQDK TSPTIDVAFA
     SAEPEKLAAA FGLSALPAGK TASAVIWTTT PWTIPANQAL NVHPDFDYGL YDTEKGLLIL
     AADLAKGALE RFGLTGVEVA RCKGQALDRL TFRHPFYDRV SPVYVGDYVT LDAGTGIVHS
     APAYGLEDFD SCRKNGMPND AILNPVTSDG TYVDSLPFFG GLHIWKANPL IVEKLAEVGA
     LMHTSPLSHS YPHCWRHKTP VVYRATTQWF VGMDREVAGS TLRQRALKGV DDTAFFPAWG
     QARLHAMIAN RPDWCVSRQR NWGVPIPFFL DKQTGEPHPR TPELLEAVAR KVEEQGINAW
     FELDPAELLG EDAARFDKMK DTLDVWFDSG TTHFHVLRGT HAEQLAYPAD LYLEGSDQHR
     GWFHSSLLTG CALDGRAPYN QLLTHGFVVD GQGRKMSKSV GNVIAPQKIN DSLGADILRL
     WVASTDYSGE LAISDTILKG TTDSYRRLRN TIRFLLANLS DFNPATDALP VSELTELDRY
     ALVLAQRLHA GVAEDCYPRY AFHTAMQAIV GYCTDDLGAF WLDIIKDRLY TTKADSKARR
     SAQTALWHVT RSLLSLLAPV LCFTADEAWQ ALTGEAEDSP VYHTWHELPV VADAEALAAR
     WDVLRALRAQ INKDIETLRE AGAVGSSLQA EVDIEADAGL YPLLNALGDE LKFVLIVSRV
     GVVPGPETRI RVSASGEQKC ERCWHYHPTV GENAEAPTLC ARCYDNIFGQ GESRSYA
//