ID D3D5R6_9ACTN Unreviewed; 591 AA.
AC D3D5R6;
DT 23-MAR-2010, integrated into UniProtKB/TrEMBL.
DT 23-MAR-2010, sequence version 1.
DT 24-JAN-2024, entry version 65.
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=FrEUN1fDRAFT_5138 {ECO:0000313|EMBL:EFC81750.1};
OS Parafrankia sp. EUN1f.
OC Bacteria; Actinomycetota; Actinomycetes; Frankiales; Frankiaceae;
OC Parafrankia.
OX NCBI_TaxID=102897 {ECO:0000313|EMBL:EFC81750.1, ECO:0000313|Proteomes:UP000004777};
RN [1] {ECO:0000313|EMBL:EFC81750.1, ECO:0000313|Proteomes:UP000004777}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=EUN1f {ECO:0000313|EMBL:EFC81750.1,
RC ECO:0000313|Proteomes:UP000004777};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Tice H., Bruce D., Goodwin L.,
RA Pitluck S., Larimer F., Land M.L., Hauser L., Beauchemin N., Sen A.,
RA Fernandez M., Tisa L.;
RT "The draft genome of Frankia sp. EUN1f.";
RL Submitted (JAN-2010) 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}.
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:EFC81750.1}.
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DR EMBL; ADGX01000095; EFC81750.1; -; Genomic_DNA.
DR RefSeq; WP_006543001.1; NZ_ADGX01000095.1.
DR AlphaFoldDB; D3D5R6; -.
DR Proteomes; UP000004777; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004422; F:hypoxanthine phosphoribosyltransferase activity; IEA:InterPro.
DR GO; GO:0016879; F:ligase activity, forming carbon-nitrogen bonds; IEA:UniProtKB-UniRule.
DR GO; GO:0006166; P:purine ribonucleoside salvage; IEA:InterPro.
DR GO; GO:0006400; P:tRNA modification; IEA:UniProtKB-UniRule.
DR CDD; cd01992; PP-ATPase; 1.
DR CDD; cd06223; PRTases_typeI; 1.
DR Gene3D; 3.40.50.2020; -; 1.
DR Gene3D; 3.40.50.620; HUPs; 1.
DR HAMAP; MF_01161; tRNA_Ile_lys_synt; 1.
DR InterPro; IPR005904; Hxn_phspho_trans.
DR InterPro; IPR000836; PRibTrfase_dom.
DR InterPro; IPR029057; PRTase-like.
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; TIGR01203; HGPRTase; 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; PF00156; Pribosyltran; 1.
DR Pfam; PF09179; TilS; 1.
DR SUPFAM; SSF52402; Adenine nucleotide alpha hydrolases-like; 1.
DR SUPFAM; SSF82829; MesJ substrate recognition domain-like; 1.
DR SUPFAM; SSF53271; PRTase-like; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_01161};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01161};
KW Glycosyltransferase {ECO:0000313|EMBL:EFC81750.1};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_01161};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_01161};
KW Transferase {ECO:0000313|EMBL:EFC81750.1};
KW tRNA processing {ECO:0000256|HAMAP-Rule:MF_01161}.
FT DOMAIN 26..197
FT /note="tRNA(Ile)-lysidine/2-thiocytidine synthase N-
FT terminal"
FT /evidence="ECO:0000259|Pfam:PF01171"
FT DOMAIN 286..352
FT /note="tRNA(Ile)-lysidine synthase substrate-binding"
FT /evidence="ECO:0000259|Pfam:PF09179"
FT DOMAIN 422..569
FT /note="Phosphoribosyltransferase"
FT /evidence="ECO:0000259|Pfam:PF00156"
FT REGION 240..280
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 365..413
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 257..271
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 397..413
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 31..36
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01161"
SQ SEQUENCE 591 AA; 62627 MW; F4B32EF5AB6E47B8 CRC64;
MPAPAVAAVR LGVRDAVADL PPGALVLVAC SGGADSLALA AAVAFVAPRR ALRAGLLTVD
HAWDDNSRAR AEDVAAQGRA LGLSLVEILA APSPRSEGAA RDERRKALLA AARRLDAQAV
LLGHTLDDQA ETVLLRLARG SGARSLSGMP ALDGLIRRPL LGLRRDQTRQ ACQFLGLPYW
EDPTNADPAF ARARTRSRVL PVLEAELGPG IAQALARTAD LLRADAEALD ELADATYFDL
TTASGPAPSG PAPDQKQDQK LEQKQKQKQE QDAAGSARAP AARVELDVEA LAGLSQAVRS
RVLRRAALTA GSSASALRAG HVWAIEELVT RWRGQRPVPL PSGVLARRTG GRIAIVGPDT
PIVAEAAESG GRGPAHPPHN QEDRPVSQAA TAKPDNDRTS HPTDESARAR IHPDIDDVLV
SQEEIAAKIA ELAARVDADY AGREILLVGV LKGAVMVMAD LSRALSVPIT MDFMAVSSYG
STTSSSGVVR ILKDLDRSIE GRDVLVVEDI IDSGLTLSWL LKNLRSRGPA SLEVLALFRK
PEAITVDVDL RYVGFDIPSA FVVGYGLDYA EHYRTLPFVG TLTPEAIARR A
//