ID   SYI_LIMF3               Reviewed;         930 AA.
AC   B2GB86;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   10-JUN-2008, sequence version 1.
DT   27-MAR-2024, entry version 102.
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=LAF_0582;
OS   Limosilactobacillus fermentum (strain NBRC 3956 / LMG 18251) (Lactobacillus
OS   fermentum).
OC   Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae;
OC   Limosilactobacillus.
OX   NCBI_TaxID=334390;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=NBRC 3956 / LMG 18251;
RX   PubMed=18487258; DOI=10.1093/dnares/dsn009;
RA   Morita H., Toh H., Fukuda S., Horikawa H., Oshima K., Suzuki T.,
RA   Murakami M., Hisamatsu S., Kato Y., Takizawa T., Fukuoka H., Yoshimura T.,
RA   Itoh K., O'Sullivan D.J., McKay L.L., Ohno H., Kikuchi J., Masaoka T.,
RA   Hattori M.;
RT   "Comparative genome analysis of Lactobacillus reuteri and Lactobacillus
RT   fermentum reveal a genomic island for reuterin and cobalamin production.";
RL   DNA Res. 15:151-161(2008).
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   -!- 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; AP008937; BAG26918.1; -; Genomic_DNA.
DR   RefSeq; WP_012391001.1; NC_010610.1.
DR   AlphaFoldDB; B2GB86; -.
DR   SMR; B2GB86; -.
DR   KEGG; lfe:LAF_0582; -.
DR   PATRIC; fig|334390.5.peg.628; -.
DR   eggNOG; COG0060; Bacteria.
DR   HOGENOM; CLU_001493_7_1_9; -.
DR   Proteomes; UP000001697; 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: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   CDD; cd00818; IleRS_core; 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; 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; 1.
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; Zinc.
FT   CHAIN           1..930
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_1000189175"
FT   REGION          1..21
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           57..67
FT                   /note="'HIGH' region"
FT   MOTIF           596..600
FT                   /note="'KMSKS' region"
FT   BINDING         555
FT                   /ligand="L-isoleucyl-5'-AMP"
FT                   /ligand_id="ChEBI:CHEBI:178002"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         599
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         889
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         892
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         909
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         912
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
SQ   SEQUENCE   930 AA;  105635 MW;  A87228F73E2C1A54 CRC64;
     MRVKDTLNLG KTKFPMRGRL PETEAQREAL WEENKVYEQR QKLNEGKPSF VLHDGPPYAN
     GPIHIGHAMN KISKDFIVRY KSMTGYRAPY VPGWDTHGLP IEHQLTKAGY DRKKMSLTEF
     RDLCQKYALE QVEIQKKGFK RLGVAGEWDH PYLTLAKEFE AAQIKVFGAF AKRGLLYQAK
     KPVYWSWSSE SALAEAEVEY HDVVAKTAFF TEQVQDGKGL LDSDTYLVGW TTTPWTIPAS
     EAVAVSADFE YALVQPSGSD RKYVVAASLL GDLAQKFNWT DYQVVKTFKG AEMEGMTTKH
     PYIDRELLVG LADYVTDDAG TGLVHTAPGY GDDDYNFGKK YNLPIFAPMN DQGVLTAENG
     PEFDGVFYQD ADDISLRLLE EHDALLLEED LEHSYPFDWR TKKPIVFRAT DQWFVSIDKM
     RDEILKAVDE VTYYPTWGKV RLRNMLKDRG DWVISRQRVW GVPLPIFYAE DGTPIMTEET
     INHVSDLFRE YGSNVWFDRE AKDLLPAGFT SEHSPNGKFT KETDIMDVWF DSGSSHQGVL
     AERDYLTYPA DMYLEGSDQY RGWFNSSLIT SVVVSGHAPY KSVLSQGFTL DQSGKKMSKS
     LGNVIDPNKV VKQMGAEIIR LWVMSADTSA DVRVSMETLQ QISESYRKLR NTFRFLLANT
     SDFGPENFVA YEKREAVDQY MTVNFNHFLA GMRDEFDRYD FLNAYKHLIN FVNNDLSSFY
     MNVAKDVLYI EPEDSHVRRS MQATFYEILS GLTKLLTPIL PHTTEEVWSY MDEPEDFVQL
     TEIPEARTFE NGNALLEKWE GFMELRSHVL KCLEEARNAK LIGRSLEASA DLYLTASQQE
     LLADLGTDAG LLCGVSALSV HDASEAPAEA ESFSDNAAVL VQAAKGEVCD RCRMTKEDVG
     SDPAYQQLCA RCAKLVRENF PQTVEEGLEK
//