MIAB_SALTY
ID MIAB_SALTY Reviewed; 474 AA.
AC Q9RCI2; Q7CQY6;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase {ECO:0000255|HAMAP-Rule:MF_01864};
DE EC=2.8.4.3 {ECO:0000255|HAMAP-Rule:MF_01864, ECO:0000305|PubMed:10572129};
DE AltName: Full=(Dimethylallyl)adenosine tRNA methylthiotransferase MiaB {ECO:0000255|HAMAP-Rule:MF_01864};
DE AltName: Full=tRNA-i(6)A37 methylthiotransferase {ECO:0000255|HAMAP-Rule:MF_01864};
GN Name=miaB {ECO:0000255|HAMAP-Rule:MF_01864, ECO:0000303|PubMed:10572129};
GN OrderedLocusNames=STM0670;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND MUTAGENESIS OF GLY-79;
RP CYS-83 AND ARG-233.
RC STRAIN=GT522;
RX PubMed=10572129; DOI=10.1128/jb.181.23.7256-7265.1999;
RA Esberg B., Leung H.-C.E., Tsui H.-C.T., Bjoerk G.R., Winkler M.E.;
RT "Identification of the miaB gene, involved in methylthiolation of
RT isopentenylated A37 derivatives in the tRNA of Salmonella typhimurium and
RT Escherichia coli.";
RL J. Bacteriol. 181:7256-7265(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
CC -!- FUNCTION: Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine
CC (i(6)A), leading to the formation of 2-methylthio-N6-
CC (dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read
CC codons beginning with uridine. {ECO:0000305|PubMed:10572129}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in
CC tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-
CC dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur
CC carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:37067, Rhea:RHEA-COMP:10375, Rhea:RHEA-COMP:10376,
CC Rhea:RHEA-COMP:14737, Rhea:RHEA-COMP:14739, ChEBI:CHEBI:13193,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:17319, ChEBI:CHEBI:17499,
CC ChEBI:CHEBI:29917, ChEBI:CHEBI:57844, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:64428, ChEBI:CHEBI:74415,
CC ChEBI:CHEBI:74417; EC=2.8.4.3; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01864, ECO:0000305|PubMed:10572129};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:37068;
CC Evidence={ECO:0000305|PubMed:10572129};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in
CC tRNA + S-adenosyl-L-methionine = 2-thio-N(6)-
CC dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur
CC carrier]-H + A + H(+) + L-methionine; Xref=Rhea:RHEA:36339,
CC Rhea:RHEA-COMP:10375, Rhea:RHEA-COMP:10377, Rhea:RHEA-COMP:14737,
CC Rhea:RHEA-COMP:14739, ChEBI:CHEBI:13193, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17319, ChEBI:CHEBI:17499, ChEBI:CHEBI:29917,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:64428,
CC ChEBI:CHEBI:74415, ChEBI:CHEBI:74416;
CC Evidence={ECO:0000250|UniProtKB:Q9WZC1};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:36340;
CC Evidence={ECO:0000250|UniProtKB:Q9WZC1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-thio-N(6)-dimethylallyladenosine(37) in tRNA + S-adenosyl-L-
CC methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA
CC + H(+) + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:37063, Rhea:RHEA-
CC COMP:10376, Rhea:RHEA-COMP:10377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:74416,
CC ChEBI:CHEBI:74417; Evidence={ECO:0000250|UniProtKB:Q9WZC1};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:37064;
CC Evidence={ECO:0000250|UniProtKB:Q9WZC1};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01864};
CC Note=Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000255|HAMAP-Rule:MF_01864};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01864}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01864}.
CC -!- SIMILARITY: Belongs to the methylthiotransferase family. MiaB
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01864}.
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DR EMBL; AJ249116; CAB62263.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL19621.1; -; Genomic_DNA.
DR RefSeq; NP_459662.1; NC_003197.2.
DR RefSeq; WP_001519200.1; NC_003197.2.
DR AlphaFoldDB; Q9RCI2; -.
DR SMR; Q9RCI2; -.
DR STRING; 99287.STM0670; -.
DR PaxDb; Q9RCI2; -.
DR DNASU; 1252190; -.
DR EnsemblBacteria; AAL19621; AAL19621; STM0670.
DR GeneID; 1252190; -.
DR KEGG; stm:STM0670; -.
DR PATRIC; fig|99287.12.peg.707; -.
DR HOGENOM; CLU_018697_2_0_6; -.
DR OMA; CEHFHIP; -.
DR PhylomeDB; Q9RCI2; -.
DR BioCyc; SENT99287:STM0670-MON; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035596; F:methylthiotransferase activity; IBA:GO_Central.
DR GO; GO:0035597; F:N6-isopentenyladenosine methylthiotransferase activity; IBA:GO_Central.
DR GO; GO:0035600; P:tRNA methylthiolation; IBA:GO_Central.
DR Gene3D; 3.40.50.12160; -; 1.
DR Gene3D; 3.80.30.20; -; 1.
DR HAMAP; MF_01864; tRNA_metthiotr_MiaB; 1.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR005839; Methylthiotransferase.
DR InterPro; IPR020612; Methylthiotransferase_CS.
DR InterPro; IPR013848; Methylthiotransferase_N.
DR InterPro; IPR038135; Methylthiotransferase_N_sf.
DR InterPro; IPR006463; MiaB_methiolase.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR023404; rSAM_horseshoe.
DR InterPro; IPR002792; TRAM_dom.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF00919; UPF0004; 1.
DR SFLD; SFLDF00273; (dimethylallyl)adenosine_tRNA; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR00089; TIGR00089; 1.
DR PROSITE; PS51449; MTTASE_N; 1.
DR PROSITE; PS01278; MTTASE_RADICAL; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
DR PROSITE; PS50926; TRAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Metal-binding; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..474
FT /note="tRNA-2-methylthio-N(6)-dimethylallyladenosine
FT synthase"
FT /id="PRO_0000359589"
FT DOMAIN 3..120
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT DOMAIN 143..375
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 378..441
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 12
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 49
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 83
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 157
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 161
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 164
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT MUTAGEN 79
FT /note="G->D: Loss of activity."
FT /evidence="ECO:0000269|PubMed:10572129"
FT MUTAGEN 83
FT /note="C->Y: Loss of activity."
FT /evidence="ECO:0000269|PubMed:10572129"
FT MUTAGEN 233
FT /note="R->H: Loss of activity at elevated temperature."
FT /evidence="ECO:0000269|PubMed:10572129"
SQ SEQUENCE 474 AA; 53716 MW; 2E5ECEED9F28D38C CRC64;
MTKKLHIKTW GCQMNEYDSS KMADLLDATH GYQLTDVAEE ADVLLLNTCS IREKAQEKVF
HQLGRWRLLK EKNPDLIIGV GGCVASQEGE HIRQRAHYVD IIFGPQTLHR LPEMINSVRG
DRSPVVDISF PEIEKFDRLP EPRAEGPTAF VSIMEGCNKY CTYCVVPYTR GEEVSRPSDD
ILFEIAQLAA QGVREVNLLG QNVNAWRGEN YDGTTGTFAD LLRLVAAIDG IDRIRFTTSH
PIEFTDDIIE VYRDTPELVS FLHLPVQSGS DRVLNLMGRT HTALEYKAII RKLRAARPDI
QISSDFIVGF PGETTDDFEK TMKLIADVNF DMSYSFIFSA RPGTPAADMV DDVPEEEKKQ
RLYILQERIN QQAMAWSRRM LGTTQRILVE GTSRKNIMEL SGRTENNRVV NFEGTPEMIG
KFVDVEITDV YPNSLRGKVV RTEDEMGLRV AETPESVIAR TRKENELGVG FYQP
