ID MIAB_BACSU Reviewed; 509 AA.
AC O31778;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 27-MAR-2024, entry version 144.
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:0000269|PubMed:20472640};
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}; Synonyms=ymcB;
GN OrderedLocusNames=BSU17010;
OS Bacillus subtilis (strain 168).
OC Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP FUNCTION AS A METHYLTHIOTRANSFERASE, AND CATALYTIC ACTIVITY.
RC STRAIN=168;
RX PubMed=20472640; DOI=10.1093/nar/gkq364;
RA Anton B.P., Russell S.P., Vertrees J., Kasif S., Raleigh E.A.,
RA Limbach P.A., Roberts R.J.;
RT "Functional characterization of the YmcB and YqeV tRNA
RT methylthiotransferases of Bacillus subtilis.";
RL Nucleic Acids Res. 38:6195-6205(2010).
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 ECO:0000269|PubMed:20472640}.
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:0000269|PubMed:20472640};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:37068;
CC Evidence={ECO:0000269|PubMed:20472640};
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; AL009126; CAB13574.1; -; Genomic_DNA.
DR PIR; D69884; D69884.
DR RefSeq; NP_389583.1; NC_000964.3.
DR RefSeq; WP_003244831.1; NZ_JNCM01000035.1.
DR AlphaFoldDB; O31778; -.
DR SMR; O31778; -.
DR STRING; 224308.BSU17010; -.
DR jPOST; O31778; -.
DR PaxDb; 224308-BSU17010; -.
DR EnsemblBacteria; CAB13574; CAB13574; BSU_17010.
DR GeneID; 939451; -.
DR KEGG; bsu:BSU17010; -.
DR PATRIC; fig|224308.179.peg.1842; -.
DR eggNOG; COG0621; Bacteria.
DR InParanoid; O31778; -.
DR OrthoDB; 9805215at2; -.
DR PhylomeDB; O31778; -.
DR BioCyc; BSUB:BSU17010-MONOMER; -.
DR Proteomes; UP000001570; 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:0035597; F:N6-isopentenyladenosine methylthiotransferase activity; IMP:UniProtKB.
DR GO; GO:0035600; P:tRNA methylthiolation; IMP:UniProtKB.
DR CDD; cd01335; Radical_SAM; 1.
DR Gene3D; 3.40.50.12160; Methylthiotransferase, N-terminal domain; 1.
DR Gene3D; 3.80.30.20; tm_1862 like domain; 1.
DR HAMAP; MF_01864; tRNA_metthiotr_MiaB; 1.
DR InterPro; IPR006638; Elp3/MiaA/NifB-like_rSAM.
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 NCBIfam; TIGR01574; miaB-methiolase; 1.
DR NCBIfam; TIGR00089; MiaB/RimO family radical SAM methylthiotransferase; 1.
DR PANTHER; PTHR43020; CDK5 REGULATORY SUBUNIT-ASSOCIATED PROTEIN 1; 1.
DR PANTHER; PTHR43020:SF2; MITOCHONDRIAL TRNA METHYLTHIOTRANSFERASE CDK5RAP1; 1.
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; SFLDG01082; B12-binding_domain_containing; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR SUPFAM; SSF102114; Radical SAM enzymes; 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..509
FT /note="tRNA-2-methylthio-N(6)-dimethylallyladenosine
FT synthase"
FT /id="PRO_0000141728"
FT DOMAIN 66..184
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT DOMAIN 207..437
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 440..503
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 75
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 111
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 145
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 221
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 225
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 228
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 509 AA; 58170 MW; 163BBCE3025F196E CRC64;
MNEKQKLESG QVHPSDKKSE KDYSKYFEAV YIPPSLKDAK KRGKEAVTYH NDFKISEQFK
GLGDGRKFYI RTYGCQMNEH DTEVMAGIFM ALGYEATNSV DDANVILLNT CAIRENAENK
VFGELGHLKA LKKNNPDLIL GVCGCMSQEE SVVNRILKKH PFVDMIFGTH NIHRLPELLS
EAYLSKEMVV EVWSKEGDVI ENLPKVRNGK IKGWVNIMYG CDKFCTYCIV PYTRGKERSR
RPEDIIQEVR RLASEGYKEI TLLGQNVNAY GKDFEDMTYG LGDLMDELRK IDIPRIRFTT
SHPRDFDDRL IEVLAKGGNL LDHIHLPVQS GSSEVLKLMA RKYDRERYME LVRKIKEAMP
NASLTTDIIV GFPNETDEQF EETLSLYREV EFDSAYTFIY SPREGTPAAK MKDNVPMRVK
KERLQRLNAL VNEISAKKMK EYEGKVVEVL VEGESKNNPD ILAGYTEKSK LVNFKGPKEA
IGKIVRVKIQ QAKTWSLDGE MVGEAIEVK
//
