ID R4YRM3_OLEAN Unreviewed; 989 AA.
AC R4YRM3;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 24-JAN-2024, entry version 57.
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 ECO:0000313|EMBL:CCK74759.1};
GN ORFNames=OLEAN_C05830 {ECO:0000313|EMBL:CCK74759.1};
OS Oleispira antarctica RB-8.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales;
OC Oceanospirillaceae; Oleispira.
OX NCBI_TaxID=698738 {ECO:0000313|EMBL:CCK74759.1, ECO:0000313|Proteomes:UP000032749};
RN [1] {ECO:0000313|EMBL:CCK74759.1, ECO:0000313|Proteomes:UP000032749}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=23877221; DOI=10.1038/ncomms3156;
RA Kube M., Chernikova T.N., Al-Ramahi Y., Beloqui A., Lopez-Cortez N.,
RA Guazzaroni M.E., Heipieper H.J., Klages S., Kotsyurbenko O.R., Langer I.,
RA Nechitaylo T.Y., Lunsdorf H., Fernandez M., Juarez S., Ciordia S.,
RA Singer A., Kagan O., Egorova O., Petit P.A., Stogios P., Kim Y.,
RA Tchigvintsev A., Flick R., Denaro R., Genovese M., Albar J.P., Reva O.N.,
RA Martinez-Gomariz M., Tran H., Ferrer M., Savchenko A., Yakunin A.F.,
RA Yakimov M.M., Golyshina O.V., Reinhardt R., Golyshin P.N.;
RT "Genome sequence and functional genomic analysis of the oil-degrading
RT bacterium Oleispira antarctica.";
RL Nat. Commun. 4:2156-2156(2013).
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}.
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DR EMBL; FO203512; CCK74759.1; -; Genomic_DNA.
DR AlphaFoldDB; R4YRM3; -.
DR STRING; 698738.OLEAN_C05830; -.
DR KEGG; oai:OLEAN_C05830; -.
DR PATRIC; fig|698738.3.peg.601; -.
DR HOGENOM; CLU_001493_7_0_6; -.
DR OrthoDB; 9810365at2; -.
DR Proteomes; UP000032749; 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 Gene3D; 1.10.730.20; -; 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_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 {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:UP000032749};
KW Zinc {ECO:0000256|HAMAP-Rule:MF_02002}.
FT DOMAIN 38..684
FT /note="Aminoacyl-tRNA synthetase class Ia"
FT /evidence="ECO:0000259|Pfam:PF00133"
FT DOMAIN 729..892
FT /note="Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase
FT anticodon-binding"
FT /evidence="ECO:0000259|Pfam:PF08264"
FT DOMAIN 951..977
FT /note="Zinc finger FPG/IleRS-type"
FT /evidence="ECO:0000259|Pfam:PF06827"
FT MOTIF 68..78
FT /note="'HIGH' region"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT MOTIF 646..650
FT /note="'KMSKS' region"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT BINDING 605
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT BINDING 649
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT BINDING 952
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT BINDING 955
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT BINDING 972
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
FT BINDING 975
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02002"
SQ SEQUENCE 989 AA; 109173 MW; 1F06E2D474EB25BB CRC64;
MSNKDQAGKV ESQYKATLNL PETNFPMRGN LAQREPELLA QWQEMGLYKQ IRNARSGREQ
FILHDGPPYA NGDIHIGHAV NKVLKDIIVK SKTMSGFDAP YVPGWDCHGL PIELKVEELV
GKAGDKVTPA EFRQHCREYA AEQVNGQREG FKRLMVLGDW ENPYLTMDFK FEANIIRTLG
KIADNGHLEK GFKPVNWCMD CGSALAEAEV EYQDKKSISI DVKFAFNDTA ALLNAFGADA
TLSDSLSSKT ASIVIWTTTP WTLPANEAVS VHPELEYSLV HINTGSEQDE ILVLATALVE
DAMSRYGITD FNVIANAAGS AFGQNLEQDS APFAVTHPFM TVAGAAKTVP VITGTHVTAD
AGTGSVHTAP MHGADDYVVC NHYGIAADTM LVSAEGAFIN NSELESLELA GLSVADKGNF
RVLGILGEKG ALIKKLKIEH SYPHCWRHKT PIIFRATPQW FIAMEAKNAE TSLLSQAMHA
VEHDIEWRPT WGKARIEGMM NGRPDWCISR QRTWGVPIAL FVHKETSALH PDSQALIEKV
ALKVEDKGID AWFELEVQDL LSAEDAENYV KVTDTLDVWF DSGVTHAAVL DERDGLRSPA
DLYLEGSDQH RGWFQSSLLT SVAAKGQAPY KTALTHGFTV DAKGRKMSKS IGNTVSPIEV
MDKLGADILR WWVADTDYST EMTVSDEILK RNADAYRRIR NTCRFLLANI AGFNPKTDLV
AVEDMLPLDA WILDRATNID LQVKALYADY NFSGLTKLLM NFSVGELGSF YLDIIKDRQY
TCKADGLARR SAQTALYHIA EAMVRWVAPV LSFTAEEIWD VLPVAVDAEG NSLEREKSVL
LAEWYELPEV KGLSLDDAYW RQIMAVKTAV NKILEEARAE KKVGSSLAAD VTLYADDALK
AQLEKLGEEL RFVTITSTAD VKALASADEA TTQKTDVSGL RLSLSASTAD KCERCWHHNV
TVGLHPEHAT LCSRCVTNIA GDGEVRHFA
//
