ID   SYI_PYRAB               Reviewed;        1067 AA.
AC   Q9V072; G8ZI86;
DT   01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   27-MAR-2024, entry version 140.
DE   RecName: Full=Isoleucine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_02003};
DE            EC=6.1.1.5 {ECO:0000255|HAMAP-Rule:MF_02003};
DE   AltName: Full=Isoleucyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_02003};
DE            Short=IleRS {ECO:0000255|HAMAP-Rule:MF_02003};
GN   Name=ileS {ECO:0000255|HAMAP-Rule:MF_02003};
GN   OrderedLocusNames=PYRAB09190; ORFNames=PAB0616;
OS   Pyrococcus abyssi (strain GE5 / Orsay).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Pyrococcus.
OX   NCBI_TaxID=272844;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=GE5 / Orsay;
RX   PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA   Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA   Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA   Weissenbach J., Zivanovic Y., Forterre P.;
RT   "An integrated analysis of the genome of the hyperthermophilic archaeon
RT   Pyrococcus abyssi.";
RL   Mol. Microbiol. 47:1495-1512(2003).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=GE5 / Orsay;
RX   PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA   Gao J., Wang J.;
RT   "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT   Pyrococcus furiosus DSM 3638.";
RL   Curr. Microbiol. 64:118-129(2012).
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_02003}.
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_02003};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_02003};
CC   -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_02003}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_02003}.
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_02003}.
CC   -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC       IleS type 2 subfamily. {ECO:0000255|HAMAP-Rule:MF_02003}.
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DR   EMBL; AJ248285; CAB49833.1; -; Genomic_DNA.
DR   EMBL; HE613800; CCE70327.1; -; Genomic_DNA.
DR   PIR; H75139; H75139.
DR   RefSeq; WP_010868042.1; NC_000868.1.
DR   AlphaFoldDB; Q9V072; -.
DR   SMR; Q9V072; -.
DR   STRING; 272844.PAB0616; -.
DR   GeneID; 1496271; -.
DR   KEGG; pab:PAB0616; -.
DR   PATRIC; fig|272844.11.peg.973; -.
DR   eggNOG; arCOG00807; Archaea.
DR   HOGENOM; CLU_001493_1_1_2; -.
DR   OrthoDB; 30823at2157; -.
DR   PhylomeDB; Q9V072; -.
DR   Proteomes; UP000000810; Chromosome.
DR   Proteomes; UP000009139; 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; cd07961; Anticodon_Ia_Ile_ABEc; 1.
DR   CDD; cd00818; IleRS_core; 1.
DR   Gene3D; 3.30.720.200; -; 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_02003; Ile_tRNA_synth_type2; 1.
DR   InterPro; IPR001412; aa-tRNA-synth_I_CS.
DR   InterPro; IPR002300; aa-tRNA-synth_Ia.
DR   InterPro; IPR033709; Anticodon_Ile_ABEc.
DR   InterPro; IPR002301; Ile-tRNA-ligase.
DR   InterPro; IPR023586; Ile-tRNA-ligase_type2.
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; PTHR42780:SF1; ISOLEUCINE--TRNA LIGASE, CYTOPLASMIC; 1.
DR   PANTHER; PTHR42780; SOLEUCYL-TRNA SYNTHETASE; 1.
DR   Pfam; PF08264; Anticodon_1; 1.
DR   Pfam; PF19302; DUF5915; 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; 2.
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..1067
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_0000098588"
FT   MOTIF           49..59
FT                   /note="'HIGH' region"
FT   MOTIF           625..629
FT                   /note="'KMSKS' region"
FT   BINDING         628
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02003"
SQ   SEQUENCE   1067 AA;  126109 MW;  B7A8C50C93924D82 CRC64;
     MIKEPEFREY DPKKLEEKVE KFWSENEIYR KVKELRKDGP KYYFLDGPPY VSGAIHLGTA
     WNKIIKDMII RFRTMQGYNV WRQPGYDMHG LPIEVKVEQA LGLKTKKEIE EKIGVENFIK
     KCKEFALNNL KIMTEQFKML GIWMDWDNPY MTIKNEYIES AWFTLKRAWE KGLLEKDKRV
     LHWCPRCETA LAEHEVRGEY KLRKDPSIYV KFPVEGKENE YLLIWTTTPW TLPANLAVSA
     HPDYDYVKVK VEFNGREEYW ILAKALVDKV LGEIGVKGEV VEEFKGRELE GLRYVHILMD
     EYPRQKEFKE KYEWAHRVIL ADFVTLEEGT GLVHTAPGHG EEDFEVGQKY GLPVYSPLDD
     QGKYTEGKWK GIYVKEADPK IIEHLREKGY LVKAGEIEHK YPHCWRCKTP LIFRATDQWF
     LKISKVKDKI IKENDEKVTW YPDWVKIRFD NGVRDSGDWV ISRQRYWGIP LPIWQSEDGE
     IYVVGSWREL VELAVAIEVN GERIELPESY EEKLKVIEEK LGPEDLHRPY VDAFIIKVNG
     KDMRRVKDVV DVWFDSGIAS WASLGYPRNK ELFEKLWPAD FIVEGEDQVT KWFYSQQAAS
     IVAFDTVPYR RVAMHGYVLD EKGDKMSKSL GNIIRPEEVV ERAGRDTFRF YMLWATNPWE
     NLKFSWKGVE QVRRMLNILW NVYVLASTYM SLDNFDPRKL NPDELPFREE DKWILSRVNS
     LISEVENGIE SFYLTKATRA LYNFVVEDLS RWYVRLIRKR LWVEGEDPDK LAAYYTLWKV
     FDVLLRLLAP FTPYIAEEIY QNLIRPFTNV ESVHMLDWPK VDEKAIDEEL EREMEFIRRI
     VEAGSAARQR AKIKLRYPVR RIIIETEDET VKKAVERLNR ILRDQLNAKE VKVGRVEREL
     TIKPNFAKLG PEFKGDAKII AKWINENGRE LYEKGELTVE IDGKTFHLTR EHIIVEEKLP
     DFFVSEEFEG GRVFVDKTLT RELIAEGLAR EFVRRIQEMR KRLDLDVNDR IIVTIETTDE
     NVELLKENLD YIMRETRADK IVFGKAKGYV VEWPEVQAKI GIEKVEE
//