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
//