ID   SYI_DESHD               Reviewed;         922 AA.
AC   B8FT35;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   03-MAR-2009, sequence version 1.
DT   27-MAR-2024, entry version 90.
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=Dhaf_4041;
OS   Desulfitobacterium hafniense (strain DSM 10664 / DCB-2).
OC   Bacteria; Bacillota; Clostridia; Eubacteriales; Desulfitobacteriaceae;
OC   Desulfitobacterium.
OX   NCBI_TaxID=272564;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 10664 / DCB-2;
RX   PubMed=22316246; DOI=10.1186/1471-2180-12-21;
RA   Kim S.H., Harzman C., Davis J.K., Hutcheson R., Broderick J.B., Marsh T.L.,
RA   Tiedje J.M.;
RT   "Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive
RT   anaerobe capable of dehalogenation and metal reduction.";
RL   BMC Microbiol. 12:21-21(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_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; CP001336; ACL22051.1; -; Genomic_DNA.
DR   RefSeq; WP_015944977.1; NC_011830.1.
DR   AlphaFoldDB; B8FT35; -.
DR   SMR; B8FT35; -.
DR   KEGG; dhd:Dhaf_4041; -.
DR   HOGENOM; CLU_001493_7_0_9; -.
DR   Proteomes; UP000007726; 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; 2.170.220.10; -; 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..922
FT                   /note="Isoleucine--tRNA ligase"
FT                   /id="PRO_1000189151"
FT   MOTIF           57..67
FT                   /note="'HIGH' region"
FT   MOTIF           594..598
FT                   /note="'KMSKS' region"
FT   BINDING         553
FT                   /ligand="L-isoleucyl-5'-AMP"
FT                   /ligand_id="ChEBI:CHEBI:178002"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT   BINDING         597
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
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         895
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"
FT   BINDING         915
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
SQ   SEQUENCE   922 AA;  104696 MW;  B643CE2C0E98E9F2 CRC64;
     MDYRNTLNLP ETDFPMRGNL PQREPEILQK WEEEDIYATV QKARAGRPKF VLHDGPPYAN
     GDIHLGHALN KVIKDIIVKY KTMAGFDAPY VPGWDTHGLP IEQQVIKKLG VNRHAVSVVE
     FRRMCKEYAK KYISIQKEQF KRLGVRGDWQ NPYLTLEKEY EAAQIGVFGK MARKKYIYKG
     LKPVYWCPSC ETALAEAEIE YAEKTSHAIY VKFPVKEGKG VLTDENTFVI IWTTTPWTLP
     ANLAITLHEE FSYVQVQVEK EHWLVAEGML ESLRSLWNLE LPVEKRFVGK ELEGVICKHP
     FIERDSVLIL GEHVTLEAGT GCVHTAPGHG EEDFNVGKKY GLPVLCPVDH QGKFTAEGGA
     YAGMKVDKAN PVIIEDLKNL HALVHEDKIK HSYAHCWRCN NPIIYRATEQ WFASIDGFRK
     AALEEIDKVQ WIPSWGKDRI YNMIADRGDW CISRQRTWGV PIPIFYCEDC GKEIISDETI
     AKVQEIFREE GSDAWFLRPA AELLPEGFTC ACGGKSFRKE TDIMDVWFDS GTSHTSVLME
     RKELAWPADL YMEGSDQHRG WFNSSLSTSV AAYGKAPYKA VLTHGFLVDE KGRKMSKSLG
     NGVDPLQVTK EMGADILRLW VCAADYKNDV AVSPRIMKQM SEAYRKIRNT LRFLLSNLND
     FDPAKDRVAY KDLPEIDRWA LLQLGKVTQR VLQGYEKYEF HWVYHSVHNF CAVELSAIYL
     DIVKDRLYVE GKNSTLRRAS QTVLYDVLNA LVRLMAPVLT YTADEIWPYV PGVPAGSHVQ
     TEEMPEALPQ WLDEALEKKW DTLLAVRSEV TKALEKARQD KLINHPLTAQ VDLYPNAELE
     GFLRGIPNLS EIFIVSAVQL HSAGEEKPEG LSMAEDLAGF GIAVNSAAGE KCERCWIYDT
     GVGENQEHPT LCPRCASVVS HL
//