ID   SYI_SHIFL               Reviewed;         938 AA.
AC   Q83MH2; Q7UDT9;
DT   20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2003, sequence version 1.
DT   24-JAN-2024, entry version 133.
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=SF0022, S0025;
OS   Shigella flexneri.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Shigella.
OX   NCBI_TaxID=623;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=301 / Serotype 2a;
RX   PubMed=12384590; DOI=10.1093/nar/gkf566;
RA   Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA   Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA   Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA   Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT   "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT   through comparison with genomes of Escherichia coli K12 and O157.";
RL   Nucleic Acids Res. 30:4432-4441(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700930 / 2457T / Serotype 2a;
RX   PubMed=12704152; DOI=10.1128/iai.71.5.2775-2786.2003;
RA   Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G.,
RA   Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T.,
RA   Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R.;
RT   "Complete genome sequence and comparative genomics of Shigella flexneri
RT   serotype 2a strain 2457T.";
RL   Infect. Immun. 71:2775-2786(2003).
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; AE005674; AAN41688.1; -; Genomic_DNA.
DR   EMBL; AE014073; AAP15570.1; -; Genomic_DNA.
DR   RefSeq; NP_705981.1; NC_004337.2.
DR   RefSeq; WP_001286898.1; NZ_WPGW01000005.1.
DR   AlphaFoldDB; Q83MH2; -.
DR   SMR; Q83MH2; -.
DR   STRING; 198214.SF0022; -.
DR   PaxDb; 198214-SF0022; -.
DR   GeneID; 1024586; -.
DR   KEGG; sfl:SF0022; -.
DR   KEGG; sfx:S0025; -.
DR   PATRIC; fig|198214.7.peg.25; -.
DR   HOGENOM; CLU_001493_7_1_6; -.
DR   Proteomes; UP000001006; Chromosome.
DR   Proteomes; UP000002673; 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; 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   Acetylation; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW   Metal-binding; Nucleotide-binding; Protein biosynthesis;
KW   Reference proteome; Zinc.
FT   CHAIN           1..938
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_0000098460"
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"
FT   MOD_RES         183
FT                   /note="N6-acetyllysine"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   CONFLICT        782
FT                   /note="R -> C (in Ref. 2; AAP15570)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   938 AA;  104267 MW;  AE849F07887B771D CRC64;
     MSDYKSTLNL PETGFPMRGD LAKREPGMLA RWTDDDLYGI IRAAKKGKKT FILHDGPPYA
     NGSIHIGHSV NKILKDIIVK SKGLSGYDSP YVPGWDCHGL PIELKVEQEY GKPGEKFTAA
     EFRAKCREYA ATQVDGQRKD FIRLGVLGDW SHPYLTMDFK TEANIIRALG KIIGNGHLHK
     GAKPVHWCVD CRSALAEAEV EYYDKTSPSI DVAFQAVDQD ALKAKFGVSN VNGPISLVIW
     TTTPWTLPAN RAISIAPDFD YALVQIDGQA VILAKDLVES VMQRIGVTDY TILGTVKGAE
     LELLRFTHPF MGFDVPAILG DHVTLDAGTG AVHTAPGHGP DDYVIGQKYG LETANPVGPD
     GTYLPGTYPT LDGVNVFKAN DIVVALLQEK GALLHVEKMQ HSYPCCWRHK TPIIFRATPQ
     WFVSMDQKGL RAQSLKEIKG VQWLPDWGQA RIESMVANRP DWCISRQRTW GVPMSLFVHK
     DTEELHPRTL ELMEEVAKRV EVDGIQAWWD LDAKEILGDE ADQYVKVPDT LDVWFDSGST
     HSSVVDVRPE FAGHAADMYL EGSDQHRGWF MSSLMISTAM KGKAPYRQVL THGFTVDGQG
     RKMSKSIGNT VSPQDVMNKL GADILRLWVA STDYTGEMAV SDEILKRAAD SYRRIRNTAR
     FLLANLNGFD PAKDMVKPEE MVVLDRWAVG CAKAAQEDIL KAYEAYDFHE VVQRLMRFCS
     VEMGSFYLDI IKDRQYTAKA DSVARRSCQT ALYHIAEALV RWMAPILSFT ADEVWGYLPG
     EREKYVFTGE WYEGLFGLAD SEAMNDAFWD ELLKVRGEVN KVIEQARADK KVGGSLEAAV
     TLYAEPELAA KLTALGDELR FVLLTSGATV ADYNDAPADA QQSEVLKGLK VALSKAEGEK
     CPRCWHYTQD VGKVAEHAEI CGRCVSNVAG DGEKRKFA
//