MIAB_RUTMC
ID MIAB_RUTMC Reviewed; 444 AA.
AC A1AX14;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 89.
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};
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}; OrderedLocusNames=Rmag_0743;
OS Ruthia magnifica subsp. Calyptogena magnifica.
OC Bacteria; Proteobacteria; Gammaproteobacteria; sulfur-oxidizing symbionts;
OC Candidatus Ruthia.
OX NCBI_TaxID=413404;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=17303757; DOI=10.1126/science.1138438;
RA Newton I.L.G., Woyke T., Auchtung T.A., Dilly G.F., Dutton R.J.,
RA Fisher M.C., Fontanez K.M., Lau E., Stewart F.J., Richardson P.M.,
RA Barry K.W., Saunders E., Detter J.C., Wu D., Eisen J.A., Cavanaugh C.M.;
RT "The Calyptogena magnifica chemoautotrophic symbiont genome.";
RL Science 315:998-1000(2007).
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:0000255|HAMAP-Rule:MF_01864}.
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};
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; CP000488; ABL02471.1; -; Genomic_DNA.
DR RefSeq; WP_011738096.1; NC_008610.1.
DR AlphaFoldDB; A1AX14; -.
DR SMR; A1AX14; -.
DR STRING; 413404.Rmag_0743; -.
DR EnsemblBacteria; ABL02471; ABL02471; Rmag_0743.
DR KEGG; rma:Rmag_0743; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_2_2_6; -.
DR OMA; CEHFHIP; -.
DR OrthoDB; 397139at2; -.
DR Proteomes; UP000002587; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035596; F:methylthiotransferase activity; IEA:InterPro.
DR GO; GO:0006400; P:tRNA modification; IEA:UniProtKB-UniRule.
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; SFLDG01061; methylthiotransferase; 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 3: Inferred from homology;
KW 4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Metal-binding; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..444
FT /note="tRNA-2-methylthio-N(6)-dimethylallyladenosine
FT synthase"
FT /id="PRO_0000374513"
FT DOMAIN 2..119
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT DOMAIN 147..379
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 382..444
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 11
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 48
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 82
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 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 165
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 168
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"
SQ SEQUENCE 444 AA; 49747 MW; 13C5FAD640F3A558 CRC64;
MKKLYIRTFG CQMNEYDSNK IADVLNHSHG LVLTDDAASA NVLLLNTCSI REKAQEKLFH
QLGRWRKLKD KNSNLIIGVG GCVASQEGEL ILERAPYVDI IFGPQTLHRL PSMLNEVLTP
TPGMSVKPSI DISFPEIEKF DHLPKPKTSS VTAFVSIMEG CSKYCTFCIV PYTRGEEVSR
PFIDVINEVK ILAIQGVREV NLLGQNVNAY QGLMDDGEIA DLALLINIAA QIDGIKRIRY
TTSHPTQFSD SLIEAYMEVP KLASHLHLPI QSGSDKILRL MKRGHMVIEY KSKIRKLRKI
RPDISISSDF IIGFPGENEQ DFLDTMTLID EIGFDKSFSF IYSARPGTLA SSYLDDVDMD
VKKQRLALVQ KTIDKNTERI SKSMVGSVQK ILVENVAKKR DNLFGRTENM RNTHFKGDKS
LIGQIVNIKI TQGRGNSLVG NLIA
