ID SYI_DECAR Reviewed; 932 AA.
AC Q47BK5;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2005, sequence version 1.
DT 27-MAR-2024, entry version 113.
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}; OrderedLocusNames=Daro_3046;
OS Dechloromonas aromatica (strain RCB).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Rhodocyclales; Azonexaceae;
OC Dechloromonas.
OX NCBI_TaxID=159087;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RCB;
RX PubMed=19650930; DOI=10.1186/1471-2164-10-351;
RA Salinero K.K., Keller K., Feil W.S., Feil H., Trong S., Di Bartolo G.,
RA Lapidus A.;
RT "Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB:
RT indications of a surprisingly complex life-style and cryptic anaerobic
RT pathways for aromatic degradation.";
RL BMC Genomics 10:351-351(2009).
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;
CC Evidence={ECO:0000255|HAMAP-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; CP000089; AAZ47776.1; -; Genomic_DNA.
DR AlphaFoldDB; Q47BK5; -.
DR SMR; Q47BK5; -.
DR STRING; 159087.Daro_3046; -.
DR KEGG; dar:Daro_3046; -.
DR eggNOG; COG0060; Bacteria.
DR HOGENOM; CLU_001493_7_1_4; -.
DR OrthoDB; 9810365at2; -.
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; 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..932
FT /note="Isoleucine--tRNA ligase"
FT /id="PRO_0000098378"
FT MOTIF 58..68
FT /note="'HIGH' region"
FT MOTIF 611..615
FT /note="'KMSKS' region"
FT BINDING 570
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
FT BINDING 614
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
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 898
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"
FT BINDING 918
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02002"
SQ SEQUENCE 932 AA; 104052 MW; 06C1ECF9BC461869 CRC64;
MADYKDSLNL PDTAFPMRGD LPKREPQWVA QWQEKKLYQR IREICAGRPR FTLHDGPPYA
NGDIHIGHAV NKVLKDIIVR SKTLSGFDAP YVPGWDCHGL PIEHQIEKLH GKAIPADKVR
ELSRAYAAEQ VERQKKDFIR LGVLGDWGNP YLTMNFSAEA GEIRALGKIL EQGYLYQGLK
PVNWCLDCGS ALAEAEVEYE DKNSPAIDVA FEVHENHTAK LAAAFGLTHL RGPAFAVIWT
TTPWTLPANE AVSVHPDLTY DLIETEKGAL ILVRELAEAA LKRYGLEGTV AGSCTGDKLD
QMLLKHPFQN RDVAIICGTH VTTEAGTGLV HTAPAHGVDD YNIGKKYGLP VNNPVGNDGK
FISTTPALSV GELAGKTVWE ANPQVLQELE ARARLLKNER IQHSYPHCWR HKTPIIFRAT
TQWFIGMENK KNEDASTLRW IAERAVDETQ FFPAWGRARL EGMMKTRPDW CVSRQRNWGV
PIPFFLHKET GQPHPRTAEL IEQVALRVEK SGIEAWFSLD AAELLGAEAD QYVKMKDTLD
VWFDSGTTHW HVMRGSHAAD HTYPADLYLE GSDQHRGWFQ SSLLSGCAID GRAPYKGLLT
HGFVVDGKGH KMSKSKGNVI APQQVSDKMG ADILRLWTAS TDYSGELTIS DEILKRVVEG
YRRIRNTLRF LLANVSDFDA ATDMLPIDQW LEIDRYALAL TRELQDGCRA DFDKYEFHRV
VQALQTFCSE DLGGFYLDIL KDRLYTTAPK SVARRSAQSA LWHITQAFVR LLAPITAFTA
EEVWQVLTGK ADDSVMFQVW HDLPALAGEG DLLAKWALIR TARADVTKAL EAQREAGKIG
SALQAAVEIH CGGEKYEALA SLGDDLKFVF ICSSTVAVRD DNEQVIATPL EHAKCERCWH
VREDVGANTE HPTLCGRCVS NLYGEGEVRG CA
//
