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Database: UniProt
Entry: A0A1Y4DDX9_9BACT
LinkDB: A0A1Y4DDX9_9BACT
Original site: A0A1Y4DDX9_9BACT 
ID   A0A1Y4DDX9_9BACT        Unreviewed;       939 AA.
AC   A0A1Y4DDX9;
DT   30-AUG-2017, integrated into UniProtKB/TrEMBL.
DT   30-AUG-2017, sequence version 1.
DT   24-JAN-2024, entry version 28.
DE   RecName: Full=Isoleucine--tRNA ligase {ECO:0000256|HAMAP-Rule:MF_02002};
DE            EC=6.1.1.5 {ECO:0000256|HAMAP-Rule:MF_02002};
DE   AltName: Full=Isoleucyl-tRNA synthetase {ECO:0000256|HAMAP-Rule:MF_02002};
DE            Short=IleRS {ECO:0000256|HAMAP-Rule:MF_02002};
GN   Name=ileS {ECO:0000256|HAMAP-Rule:MF_02002};
GN   ORFNames=B5F75_00580 {ECO:0000313|EMBL:OUO57307.1};
OS   Elusimicrobium sp. An273.
OC   Bacteria; Elusimicrobiota; Elusimicrobia; Elusimicrobiales;
OC   Elusimicrobiaceae; Elusimicrobium.
OX   NCBI_TaxID=1965617 {ECO:0000313|EMBL:OUO57307.1, ECO:0000313|Proteomes:UP000196368};
RN   [1] {ECO:0000313|Proteomes:UP000196368}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=An273 {ECO:0000313|Proteomes:UP000196368};
RA   Medvecky M., Cejkova D., Polansky O., Karasova D., Kubasova T., Cizek A.,
RA   Rychlik I.;
RT   "Function of individual gut microbiota members based on whole genome
RT   sequencing of pure cultures obtained from chicken caecum.";
RL   Submitted (APR-2017) to the EMBL/GenBank/DDBJ databases.
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:0000256|ARBA:ARBA00025217, ECO:0000256|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;
CC         Evidence={ECO:0000256|ARBA:ARBA00000114, ECO:0000256|HAMAP-
CC         Rule:MF_02002};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_02002};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000256|HAMAP-Rule:MF_02002};
CC   -!- SUBUNIT: Monomer. {ECO:0000256|HAMAP-Rule:MF_02002}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|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:0000256|HAMAP-Rule:MF_02002}.
CC   -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC       IleS type 1 subfamily. {ECO:0000256|ARBA:ARBA00006887,
CC       ECO:0000256|HAMAP-Rule:MF_02002}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:OUO57307.1}.
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DR   EMBL; NFJD01000001; OUO57307.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A1Y4DDX9; -.
DR   OrthoDB; 9810365at2; -.
DR   Proteomes; UP000196368; Unassembled WGS sequence.
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   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 {ECO:0000256|ARBA:ARBA00023146,
KW   ECO:0000256|HAMAP-Rule:MF_02002};
KW   ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW   Rule:MF_02002};
KW   Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_02002};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_02002};
KW   Metal-binding {ECO:0000256|HAMAP-Rule:MF_02002};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW   Rule:MF_02002};
KW   Protein biosynthesis {ECO:0000256|ARBA:ARBA00022917, ECO:0000256|HAMAP-
KW   Rule:MF_02002}; Reference proteome {ECO:0000313|Proteomes:UP000196368};
KW   Zinc {ECO:0000256|HAMAP-Rule:MF_02002}.
FT   DOMAIN          29..645
FT                   /note="Aminoacyl-tRNA synthetase class Ia"
FT                   /evidence="ECO:0000259|Pfam:PF00133"
FT   DOMAIN          689..847
FT                   /note="Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase
FT                   anticodon-binding"
FT                   /evidence="ECO:0000259|Pfam:PF08264"
FT   MOTIF           60..70
FT                   /note="'HIGH' region"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT   MOTIF           606..610
FT                   /note="'KMSKS' region"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT   BINDING         565
FT                   /ligand="L-isoleucyl-5'-AMP"
FT                   /ligand_id="ChEBI:CHEBI:178002"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT   BINDING         609
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT   BINDING         897
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT   BINDING         900
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT   BINDING         917
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT   BINDING         920
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
SQ   SEQUENCE   939 AA;  106383 MW;  9A2A8F96B5ABFFC1 CRC64;
     MAKNKYSHTV LLPKTDFPMR AGLAQKEPKI LEFWQSIHLY EAMLKKNEAG KHFVLHDGPP
     YANGKIHIGH ALDKTIKDII IKSRAMTGYY TPYVPGWDCH GLPIEQALLK ELKQDKKHIT
     DVPAFRKKAR AFAAKFIDLQ RQGFKRLGVQ GDWDNPYLTM SPRYEGITIG VFLDLIEKGY
     VYKGQKTITW CSHCETALAD AETEYKDVKS SSIYLRFKLV DPKKEIFGDL DYTKPVSLAV
     WTTTPWTIPS NMAAAVSNTE DYAVLKDEKT GEYYIVAEKL AEEFLKNTGL DCTQAGKVAG
     ADLVGLKYYH PLTHKENPVI WTDFVTMDAG VGIVHIAPGH GEDDFRAGKQ WGLETFCPVD
     EKGCYTKEAG VFEGMHVFDA NPLMVKKLDE LGALIKEQEI THSYPHCWRC HNPIIFRATE
     QWFMSIDKDG LRQKLMDNLS NVKFYPAGGE ERMRSMIALR PDWCLSRQRF WGTPVTVLYC
     KKCGKPQVNH ELFAFIKERA MKEGSDFWFI DPVEKLMPQG YHCECGCGEF RKETDILDVW
     LDSGVSWAAV VKDRGMSFPA DVYSEGSDQH RGWFQSSYIP SFTLEGTAPF KTILTHGMVL
     DQQGRPMHKS LGNSVDPEDV INKYGADILR LWVAFSDYQG DVRISDEILG GPVDTYRKIR
     NTVRYALGNL SDYDPALHRV PAKELAEMDQ YMLGRLNELI QEVHAGYSEF NFRRAIRAIT
     DFCILDLSSF MLDASKDRLY TLGASSAARR SAQTVLAEIA VTLLQLMAPV LSFTAEEAWQ
     ELRKTALGRD LPQSIFLSNM PANASMIPDV KLEEKWNKIR RVRETVQKVL EETRQKGVIG
     SSLEAKVTFK TSNPEMKAFL EETKALWPEI AIVSEVEIAD GKEELEVTAE HAAGQKCARC
     WQWKREVGSV PGHADLCARC ADVLEKEGIK VEEEEQVRA
//
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