ID   SYI_BRADU               Reviewed;        1002 AA.
AC   Q89DF8;
DT   20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2003, sequence version 1.
DT   03-AUG-2022, entry version 111.
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=blr7481;
OS   Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS   NBRC 14792 / USDA 110).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Bradyrhizobiaceae; Bradyrhizobium.
OX   NCBI_TaxID=224911;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX   PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA   Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA   Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA   Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT   "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT   Bradyrhizobium japonicum USDA110.";
RL   DNA Res. 9:189-197(2002).
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; BA000040; BAC52746.1; -; Genomic_DNA.
DR   RefSeq; NP_774121.1; NC_004463.1.
DR   RefSeq; WP_011090213.1; NZ_CP011360.1.
DR   AlphaFoldDB; Q89DF8; -.
DR   SMR; Q89DF8; -.
DR   STRING; 224911.27355764; -.
DR   EnsemblBacteria; BAC52746; BAC52746; BAC52746.
DR   GeneID; 64027238; -.
DR   KEGG; bja:blr7481; -.
DR   PATRIC; fig|224911.44.peg.7581; -.
DR   eggNOG; COG0060; Bacteria.
DR   HOGENOM; CLU_001493_7_1_5; -.
DR   InParanoid; Q89DF8; -.
DR   OMA; HLGTAWN; -.
DR   PhylomeDB; Q89DF8; -.
DR   Proteomes; UP000002526; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
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; IBA:GO_Central.
DR   GO; GO:0000049; F:tRNA binding; IEA:InterPro.
DR   GO; GO:0006428; P:isoleucyl-tRNA aminoacylation; IBA:GO_Central.
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..1002
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_0000098360"
FT   MOTIF           70..80
FT                   /note="'HIGH' region"
FT   MOTIF           671..675
FT                   /note="'KMSKS' region"
FT   BINDING         630
FT                   /ligand="L-isoleucyl-5'-AMP"
FT                   /ligand_id="ChEBI:CHEBI:178002"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         674
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
SQ   SEQUENCE   1002 AA;  112383 MW;  41ABFF403E52F837 CRC64;
     MSEKPQKSQK SEVKDYSKTL FLPQTEFPMR AGLPQREPEI LKYWNDIGLY DRLRQEAEGR
     TKFVLHDGPP YANGNIHIGH ALNKILKDVV TKSQQMLGFD SNYVPGWDCH GLPIEWKIEE
     ENYRKKGKQK PDFRDSAAMV AFRKECRAYA THWINVQREE FKRLGIIGDW DHPYQTMSYP
     AEAQIARELM KFAANGTLYR GSKPVMWSVV EKTALAEAEV EYEDYTSDMV WVKFPVTSPA
     HGALASASVV IWTTTPWTLP GNRAISFSPK IAYGLYKVTD APADNWAKTG DLLILADALA
     AEVFKQARVT TYEKVRELPA DTLDAVECAH PLKGFSGGYE FTVPLLPGDH VTDDTGTGFV
     HTAPGHGRED FDVWMANARE LEARGINTTI PYTVDENGAF TDHAPGFVGK RVINDKGEKG
     DANEAVIKAL IDAGKLLARG RLKHQYPHSW RSKKPVIFRN TPQWFIAMDK DISANGHAKK
     GDTLRARALH AISVTQWVPP SGENRINGMI ANRPDWVISR QRAWGVPIAV FVREKSDGSA
     EILQDEIVNQ RIAEAFMEEG ADAWYMDGAR ERFLGSRASE DWKKVDDICD VWFDSGSTHA
     FVLEDRQNFP QLGNIVRKVD GGSDTVMYLE GSDQHRGWFH SSLLESAGTR GRAPYDIVLT
     HGFTLDENGR KMSKSLGNTV EPQKVIKDSG ADILRLWVCA TDYADDQRIG PEILKNTIET
     YRKLRNSIRW MLGTLHHFKP SEKVAYAEMP ELERLMLHEL AGHAETVRNA YAAFDYKTVV
     ASLAAFMNSE LSAFYFDIRK DTLYCDPPSS PARKAALTTI DLLCDAILKW LAPILSFTTD
     EAWRMFRPNA EPSVHLTLFP ADIEKLRDDK LAAKWETIRN VRRAVTGALE LERAAKNIGS
     SLEASPVIYV ADRDMLATLF DTDLAEVCIT SNYEVRESEA PASAFRLDAV PGVAVVVEKA
     VGTKCARSWK ISQTVGEDPE YPDVTPRDAQ ALREWKALGV GV