ID   SYI_YERPP               Reviewed;         938 AA.
AC   A4TQF3;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   15-MAY-2007, sequence version 1.
DT   27-MAR-2024, entry version 97.
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=YPDSF_3157;
OS   Yersinia pestis (strain Pestoides F).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Yersiniaceae; Yersinia.
OX   NCBI_TaxID=386656;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Pestoides F;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Di Bartolo G., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Worsham P., Chu M., Bearden S., Garcia E.,
RA   Richardson P.;
RT   "Complete sequence of chromosome of Yersinia pestis Pestoides F.";
RL   Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000668; ABP41515.1; -; Genomic_DNA.
DR   RefSeq; WP_002210509.1; NZ_CP009715.1.
DR   AlphaFoldDB; A4TQF3; -.
DR   SMR; A4TQF3; -.
DR   GeneID; 66842962; -.
DR   KEGG; ypp:YPDSF_3157; -.
DR   PATRIC; fig|386656.14.peg.1194; -.
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; 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..938
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_1000022146"
FT   MOTIF           58..68
FT                   /note="'HIGH' region"
FT   MOTIF           602..606
FT                   /note="'KMSKS' region"
FT   BINDING         561
FT                   /ligand="L-isoleucyl-5'-AMP"
FT                   /ligand_id="ChEBI:CHEBI:178002"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         605
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         901
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         904
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         921
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         924
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
SQ   SEQUENCE   938 AA;  104690 MW;  827A66208EE0B84A CRC64;
     MSDYKNTLNL PETGFPMRGD LAKREPDMLK RWYEQDLYGI IRAAKKGKKT FILHDGPPYA
     NGNIHIGHSV NKILKDIIVK SKGMAGYDSP YIPGWDCHGL PIELKVEQLI GKPGEKVSAA
     EFRTACRKYA AEQVEGQKKD FIRLGVLGDW DHPYLTMDFK TEANIIRALS KIIDNGHLHK
     GAKPVHWCTD CGSSLAEAEV EYYDKTSQSI DVRFNAVDTA TVAAKFGVSA VNGPISLVIW
     TTTPWTLPAN RAISLNAEYL YQLVQVEGEC LILAADLVES VMKRAGITQW AVLGSCTGSD
     LELLRFTHPF MGFDVPAILG DHVTLDAGTG AVHTAPGHGP DDFVIGQKYG LEVANPVGPN
     GCYLAGTYPT LDGLFVFKAN DVVVELLREK GALLHVEKLL HSYPCCWRHK TPIIFRATPQ
     WFISMDQKGL RKQSLQEIKG VQWIPDWGQA RIETMVANRP DWCISRQRTW GVPMSLFVHK
     ETEQLHPRSI ELMEEVAKRV EQDGIQAWWD LDPAEILGAD AADYVKVPDT LDVWFDSGST
     HSSVVDVRPE FGGHSPDMYL EGSDQHRGWF MSSLMIATAM KGKAPYRQVL THGFTVDGQG
     RKMSKSIGNT ISPQDVMNKL GGDILRLWVA STDYTGEIAV SDEILKRSAD SYRRIRNTAR
     FLLANLNGFD PAQHQVKPEE MVVVDRWAVG RAQAAQAEIM EAYENYDFHL VVQRLMQFCS
     VEMGSFYLDI IKDRQYTAKG DGIARRSCQT ALFHIAEALV RWMAPIMSFT ADEIWNHLPG
     ERQQYVFTEE WYDGLFGLAG NESMNDTFWA ELLKVRGEVN KVLEQARSDK RIGGSLEAAV
     TLYAEPELAA RLNSLQDELR FVLLTSAAKV AAYADAGNDA QQSELIAGLK ITFNKADGEK
     CPRCWHYTQD VGLVAEHAEL CGRCVTNVAG DGEERKFA
//