ID   SYI_ZYMMO               Reviewed;         941 AA.
AC   Q5NQQ7; Q9RNJ5;
DT   20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-2005, sequence version 1.
DT   27-MAR-2024, entry version 119.
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=ZMO0323;
OS   Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC   Zymomonadaceae; Zymomonas.
OX   NCBI_TaxID=264203;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 31821 / ZM4 / CP4;
RA   Lee H.J., Kang H.S.;
RL   Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 31821 / ZM4 / CP4;
RX   PubMed=15592456; DOI=10.1038/nbt1045;
RA   Seo J.-S., Chong H., Park H.S., Yoon K.-O., Jung C., Kim J.J., Hong J.H.,
RA   Kim H., Kim J.-H., Kil J.-I., Park C.J., Oh H.-M., Lee J.-S., Jin S.-J.,
RA   Um H.-W., Lee H.-J., Oh S.-J., Kim J.Y., Kang H.L., Lee S.Y., Lee K.J.,
RA   Kang H.S.;
RT   "The genome sequence of the ethanologenic bacterium Zymomonas mobilis
RT   ZM4.";
RL   Nat. Biotechnol. 23:63-68(2005).
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; AF180145; AAD56932.1; -; Genomic_DNA.
DR   EMBL; AE008692; AAV88947.1; -; Genomic_DNA.
DR   RefSeq; WP_011240252.1; NZ_CP035711.1.
DR   AlphaFoldDB; Q5NQQ7; -.
DR   SMR; Q5NQQ7; -.
DR   STRING; 264203.ZMO0323; -.
DR   KEGG; zmo:ZMO0323; -.
DR   eggNOG; COG0060; Bacteria.
DR   HOGENOM; CLU_001493_7_1_5; -.
DR   Proteomes; UP000001173; 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   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   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   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..941
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_0000098513"
FT   MOTIF           69..79
FT                   /note="'HIGH' region"
FT   MOTIF           630..634
FT                   /note="'KMSKS' region"
FT   BINDING         589
FT                   /ligand="L-isoleucyl-5'-AMP"
FT                   /ligand_id="ChEBI:CHEBI:178002"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         633
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         915
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         918
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         932
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         935
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   CONFLICT        92..94
FT                   /note="SQT -> TKP (in Ref. 1; AAD56932)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        140
FT                   /note="E -> K (in Ref. 1; AAD56932)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        181
FT                   /note="A -> S (in Ref. 1; AAD56932)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   941 AA;  106263 MW;  645DF7E9C0E82279 CRC64;
     MSDQKSADAT QARDWRPTVF LPKTSFPMKA GLAKKEPEIL ARWQKEDLYQ QLREQRKGAE
     RFILHDGPPY ANGDIHIGHA LNKILKDIIM RSQTLLGKDV PYIPGWDCHG LPIEWKVEEQ
     FRKKKLNVDK DVNAVEFRQE CRKYAVHWVD TQRQEFKRLG VLGEWDNPYL TMNFEAEAII
     AGELMRFSET GQIYRGAKPV LWSVVEKTAL AEAEVDYADV DSTTIDLAFK ITDSKIPELV
     GGYAVIWTTT PWTIPANRAL AYGPDIDYVL VDLNGKHYLF AEALLEDSLK RIGHEGDAPV
     LWRGKGAELD GSIAQHPMFE KGGFFAEPRP FLGGSHVTTE AGTGIVHMAP DYGEDDFLLC
     KAHNIDPVFA VEDDGRYRKD WLWMGGEGLV ISPKINAADG PICSDLREVG ALLATSVLHH
     SYPHSWRSKA KLIYRCTPQW FIALDRPVEK GAIAGKTLRE TALKAIDEVS WFPAKGKNRI
     QTMVEGRPDW VISRQRAWGV PITLYVNRES GDYLRDPEVN ARILAAFRKE GADAWFKANH
     QLFLGDKYRL EDYEPVNDIL DVWFDSGSTH AFVVEARYGE GTRAQLYLEG SDQHRGWFQS
     SLLESCGSRG HAPYEAVLTH GFTLDGTGRK MSKSVGNVID PLKVINESGA DILRMWVAST
     DYNEDVRISK EVLSGTSDGY RKLRNSFRYL LGALEGFSEE EKVDLADLPE LEKYILHLLA
     ELDQALHESV NGFAFNRYLR LLSDFVNNDL SAFFFDIRKD RLYCDVGEAA PQGTEERRAY
     RTVLDILFHA LVRYAAPILC FTAEEVWLHR FPDAGSVHLS VWPEVDGQWK NAVLGEKWAV
     IREQRQIVTE KIEPLRREKI VGSSLEAEVT LPVDAATAKI LSSVDFSEIC ITAKINLVDA
     SDAAITVDRT QNHKCGRCWQ HLPEVEEDGA LCDRCKSVVG E
//