ID M5DPV3_9GAMM Unreviewed; 425 AA.
AC M5DPV3;
DT 29-MAY-2013, integrated into UniProtKB/TrEMBL.
DT 29-MAY-2013, sequence version 1.
DT 24-JAN-2024, entry version 51.
DE RecName: Full=tRNA(Ile)-lysidine synthase {ECO:0000256|HAMAP-Rule:MF_01161};
DE EC=6.3.4.19 {ECO:0000256|HAMAP-Rule:MF_01161};
DE AltName: Full=tRNA(Ile)-2-lysyl-cytidine synthase {ECO:0000256|HAMAP-Rule:MF_01161};
DE AltName: Full=tRNA(Ile)-lysidine synthetase {ECO:0000256|HAMAP-Rule:MF_01161};
GN Name=tilS {ECO:0000256|HAMAP-Rule:MF_01161,
GN ECO:0000313|EMBL:CCU71182.1};
GN ORFNames=TOL_0744 {ECO:0000313|EMBL:CCU71182.1};
OS Thalassolituus oleivorans MIL-1.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales;
OC Oceanospirillaceae; Thalassolituus.
OX NCBI_TaxID=1298593 {ECO:0000313|EMBL:CCU71182.1, ECO:0000313|Proteomes:UP000011866};
RN [1] {ECO:0000313|EMBL:CCU71182.1, ECO:0000313|Proteomes:UP000011866}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MIL-1 {ECO:0000313|EMBL:CCU71182.1,
RC ECO:0000313|Proteomes:UP000011866};
RX PubMed=23599290; DOI=10.1128/genomeA.00141-13;
RA Golyshin P.N., Werner J., Chernikova T.N., Tran H., Ferrer M.,
RA Yakimov M.M., Teeling H., Golyshina O.V.;
RT "Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T).";
RL Genome Announc. 1:1-3(2013).
CC -!- FUNCTION: Ligates lysine onto the cytidine present at position 34 of
CC the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an
CC ATP-dependent manner. Cytidine is converted to lysidine, thus changing
CC the amino acid specificity of the tRNA from methionine to isoleucine.
CC {ECO:0000256|HAMAP-Rule:MF_01161}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + cytidine(34) in tRNA(Ile2) + L-lysine = AMP +
CC diphosphate + H(+) + lysidine(34) in tRNA(Ile2);
CC Xref=Rhea:RHEA:43744, Rhea:RHEA-COMP:10625, Rhea:RHEA-COMP:10670,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:32551,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:82748, ChEBI:CHEBI:83665,
CC ChEBI:CHEBI:456215; EC=6.3.4.19;
CC Evidence={ECO:0000256|ARBA:ARBA00000047, ECO:0000256|HAMAP-
CC Rule:MF_01161};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496,
CC ECO:0000256|HAMAP-Rule:MF_01161}.
CC -!- DOMAIN: The N-terminal region contains the highly conserved SGGXDS
CC motif, predicted to be a P-loop motif involved in ATP binding.
CC {ECO:0000256|HAMAP-Rule:MF_01161}.
CC -!- SIMILARITY: Belongs to the tRNA(Ile)-lysidine synthase family.
CC {ECO:0000256|HAMAP-Rule:MF_01161}.
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DR EMBL; HF680312; CCU71182.1; -; Genomic_DNA.
DR AlphaFoldDB; M5DPV3; -.
DR STRING; 187493.CN03_14370; -.
DR KEGG; tol:TOL_0744; -.
DR PATRIC; fig|1298593.3.peg.717; -.
DR eggNOG; COG0037; Bacteria.
DR HOGENOM; CLU_018869_2_0_6; -.
DR Proteomes; UP000011866; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016879; F:ligase activity, forming carbon-nitrogen bonds; IEA:UniProtKB-UniRule.
DR GO; GO:0006400; P:tRNA modification; IEA:UniProtKB-UniRule.
DR CDD; cd01992; PP-ATPase; 1.
DR Gene3D; 1.20.59.20; -; 1.
DR Gene3D; 3.40.50.620; HUPs; 1.
DR HAMAP; MF_01161; tRNA_Ile_lys_synt; 1.
DR InterPro; IPR012796; Lysidine-tRNA-synth_C.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR011063; TilS/TtcA_N.
DR InterPro; IPR012094; tRNA_Ile_lys_synt.
DR InterPro; IPR012795; tRNA_Ile_lys_synt_N.
DR InterPro; IPR015262; tRNA_Ile_lys_synt_subst-bd.
DR NCBIfam; TIGR02433; lysidine_TilS_C; 1.
DR NCBIfam; TIGR02432; lysidine_TilS_N; 1.
DR PANTHER; PTHR43033; TRNA(ILE)-LYSIDINE SYNTHASE-RELATED; 1.
DR PANTHER; PTHR43033:SF1; TRNA(ILE)-LYSIDINE SYNTHASE-RELATED; 1.
DR Pfam; PF01171; ATP_bind_3; 1.
DR Pfam; PF09179; TilS; 1.
DR Pfam; PF11734; TilS_C; 1.
DR SMART; SM00977; TilS_C; 1.
DR SUPFAM; SSF52402; Adenine nucleotide alpha hydrolases-like; 1.
DR SUPFAM; SSF82829; MesJ substrate recognition domain-like; 1.
DR SUPFAM; SSF56037; PheT/TilS domain; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_01161};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01161};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_01161};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_01161};
KW Reference proteome {ECO:0000313|Proteomes:UP000011866};
KW tRNA processing {ECO:0000256|HAMAP-Rule:MF_01161}.
FT DOMAIN 354..423
FT /note="Lysidine-tRNA(Ile) synthetase C-terminal"
FT /evidence="ECO:0000259|SMART:SM00977"
FT BINDING 13..18
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01161"
SQ SEQUENCE 425 AA; 47597 MW; DB762A29EB787B99 CRC64;
MLGEEGRLIV GFSGGLDSSV LLHALAQNDG LKARLIALHV HHGLSPNADV WEAHCQAVSE
NLGVAFISAR VTVTGDGNGI EQAARNARYD VFQQHANSHD LVLVAHHNDD QVETFFQRLF
RGSGLTGLAS MAAVRPLFDD SDVLLVRPLL HVSRKQLEAY AQAQQLAWVE DESNTDTRYE
RNWWRNELLP QIWQRFTGRE ESLKRTLEQL QSDQALLQEL LKPEIDACIA YCDWPGTNEL
ICSIAALNDK PKHHRPYLLR GWLAGCGVPM PSAAMLERIQ REVIEAAEDR NPQVVLGDIC
VRRYQQHLYV TRQLDDVTPC IIDLGSNTRF PWAGSTITVT NTSEEGLASG RYDLIPAYSC
VGQTLRPAGR PQKTLKHIWQ ENSIPPWLRD RWPLLLQDGK LCAVVGICND QSVVVAHGYA
VKWLS
//
