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MIAB_VIBC3
ID   MIAB_VIBC3              Reviewed;         474 AA.
AC   A5F2X6; C3LYX3;
DT   05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   12-JUN-2007, sequence version 1.
DT   03-AUG-2022, entry version 91.
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};
GN   OrderedLocusNames=VC0395_A0484, VC395_0977;
OS   Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 /
OS   O395).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=345073;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 39541 / Classical Ogawa 395 / O395;
RA   Heidelberg J.;
RL   Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 39541 / Classical Ogawa 395 / O395;
RX   PubMed=19115014; DOI=10.1371/journal.pone.0004053;
RA   Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J.,
RA   Wang W., Wang J., Qian W., Li D., Wang L.;
RT   "A recalibrated molecular clock and independent origins for the cholera
RT   pandemic clones.";
RL   PLoS ONE 3:E4053-E4053(2008).
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; CP000627; ABQ21901.1; -; Genomic_DNA.
DR   EMBL; CP001235; ACP08989.1; -; Genomic_DNA.
DR   RefSeq; WP_000038553.1; NZ_JAACZH010000005.1.
DR   AlphaFoldDB; A5F2X6; -.
DR   SMR; A5F2X6; -.
DR   STRING; 345073.VC395_0977; -.
DR   EnsemblBacteria; ABQ21901; ABQ21901; VC0395_A0484.
DR   GeneID; 57739651; -.
DR   KEGG; vco:VC0395_A0484; -.
DR   KEGG; vcr:VC395_0977; -.
DR   PATRIC; fig|345073.21.peg.947; -.
DR   eggNOG; COG0621; Bacteria.
DR   HOGENOM; CLU_018697_2_0_6; -.
DR   OMA; CEHFHIP; -.
DR   Proteomes; UP000000249; Chromosome 2.
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; 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   3: Inferred from homology;
KW   4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Metal-binding;
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_0000374630"
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   REGION          455..474
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
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"
SQ   SEQUENCE   474 AA;  53613 MW;  C1C5DF73CC96C467 CRC64;
     MSKKLLIKTW GCQMNEYDSS KMADLLNAAN GYELTEIPEE ADVLLLNTCS IREKAQEKVF
     HQLGRWKTLK DKKPGVVIGV GGCVATQEGD SIRDRAPYVD VIFGPQTLHR LPEMIKQSQT
     SDAPVMDISF PEIEKFDRLP EPRAEGPTAF VSIMEGCSKY CTYCVVPYTR GEEVSRPMDD
     VLFEIAQLAE QGVREVNLLG QNVNAYRGAT HDGGICSFAE LLRLVATIDG IDRIRFTTSH
     PLEFTDDIIA VYEDTPELVS FLHLPVQSGS DRILTMMKRP HTAIEYKSII RKLRKARPDI
     QISSDFIVGF PGETDKDFQD TMKLIRDVDF DMSFSFIFSP RPGTPAADYP CDLSEEVKKE
     RLYELQQQIN SQAMRYSRLM LGTEQRILVE GPSKKDLMEL RGRTENNRVV NFEGSPDLIG
     QFVDVKIVDV FPNSLRGELL RTEQEMNLRI ATSPSEMKAK TRREDELGVA TFTP
 
 
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