ID A0A348HD24_9GAMM Unreviewed; 437 AA.
AC A0A348HD24;
DT 07-NOV-2018, integrated into UniProtKB/TrEMBL.
DT 07-NOV-2018, sequence version 1.
DT 24-JAN-2024, entry version 19.
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 ORFNames=ZBT109_0750 {ECO:0000313|EMBL:BBG29526.1};
OS Zymobacter palmae.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales;
OC Halomonadaceae; Zymobacter group; Zymobacter.
OX NCBI_TaxID=33074 {ECO:0000313|EMBL:BBG29526.1, ECO:0000313|Proteomes:UP000267342};
RN [1] {ECO:0000313|EMBL:BBG29526.1, ECO:0000313|Proteomes:UP000267342}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IAM14233 {ECO:0000313|EMBL:BBG29526.1,
RC ECO:0000313|Proteomes:UP000267342};
RA Yanase H.;
RT "Zymobacter palmae IAM14233 (=T109) whole genome analysis.";
RL Submitted (SEP-2018) to the EMBL/GenBank/DDBJ databases.
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; AP018933; BBG29526.1; -; Genomic_DNA.
DR RefSeq; WP_051523839.1; NZ_AP018933.1.
DR AlphaFoldDB; A0A348HD24; -.
DR STRING; 1123510.GCA_000620025_02191; -.
DR KEGG; zpl:ZBT109_0750; -.
DR OrthoDB; 9807403at2; -.
DR Proteomes; UP000267342; 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 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:UP000267342};
KW tRNA processing {ECO:0000256|HAMAP-Rule:MF_01161}.
FT DOMAIN 36..217
FT /note="tRNA(Ile)-lysidine/2-thiocytidine synthase N-
FT terminal"
FT /evidence="ECO:0000259|Pfam:PF01171"
FT DOMAIN 265..328
FT /note="tRNA(Ile)-lysidine synthase substrate-binding"
FT /evidence="ECO:0000259|Pfam:PF09179"
FT DOMAIN 367..428
FT /note="Lysidine-tRNA(Ile) synthetase C-terminal"
FT /evidence="ECO:0000259|Pfam:PF11734"
FT BINDING 41..46
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01161"
SQ SEQUENCE 437 AA; 47929 MW; EA3D8099FA2DF6AF CRC64;
MAPCPDVLAD LHGSAEPLLK TVVEALASLP SCCSRLWVAL SGGCDSITLL HCTARALRLL
PSSSLELHAL HVNHQLQDAA AAFERLCCST CAEWGVTLHI ERVTIDSDAD GGPEAQARDA
RYAAFMKVLR KDDVLWMAHH ADDQAETVLQ RAMRGSGIAG MAGMPAQRPL GRALLMRPLL
AHRQQALGAY ARRHGLRWCD DPSNASSQYD RNYLRHQVIP CLSERWPQAV AALGQVAAHA
REAHELLEMM ADRQLAQWPK APQQLPINAL STMSDSEARL MIRRALAHQG IPMPPRARLE
TVLAQLKVGH GHIHWPGGEV RLWQGALYLA ANSADGAVLS SATIDAYAQW RVEPLIAGDV
SLDVRFVARE GGERLRVNGC RRSIKALFQA RGVPPWLRER FRVAWVGETP VALVSDTDAI
VADGWHAWRD GTVCGRE
//
