MIAB_THEMA
ID MIAB_THEMA Reviewed; 443 AA.
AC Q9WZC1;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 127.
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:12766153, ECO:0000269|PubMed:15339930};
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:12766153};
GN OrderedLocusNames=TM_0653;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND SUBUNIT.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=12766153; DOI=10.1074/jbc.m301518200;
RA Pierrel F., Hernandez H.L., Johnson M.K., Fontecave M., Atta M.;
RT "MiaB protein from Thermotoga maritima. Characterization of an extremely
RT thermophilic tRNA-methylthiotransferase.";
RL J. Biol. Chem. 278:29515-29524(2003).
RN [3]
RP FUNCTION AS A METHYLTHIOTRANSFERASE, AND CATALYTIC ACTIVITY.
RX PubMed=15339930; DOI=10.1074/jbc.m408562200;
RA Pierrel F., Douki T., Fontecave M., Atta M.;
RT "MiaB protein is a bifunctional radical-S-adenosylmethionine enzyme
RT involved in thiolation and methylation of tRNA.";
RL J. Biol. Chem. 279:47555-47563(2004).
RN [4]
RP COFACTOR, AND MUTAGENESIS OF CYS-10; CYS-150; CYS-154 AND CYS-157.
RX PubMed=17407324; DOI=10.1021/bi7000449;
RA Hernandez H.L., Pierrel F., Elleingand E., Garcia-Serres R., Huynh B.H.,
RA Johnson M.K., Fontecave M., Atta M.;
RT "MiaB, a bifunctional radical-S-adenosylmethionine enzyme involved in the
RT thiolation and methylation of tRNA, contains two essential [4Fe-4S]
RT clusters.";
RL Biochemistry 46:5140-5147(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 ECO:0000269|PubMed:12766153, ECO:0000269|PubMed:15339930}.
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:12766153,
CC ECO:0000269|PubMed:15339930};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:37068;
CC Evidence={ECO:0000269|PubMed:12766153, ECO:0000269|PubMed:15339930};
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:0000269|PubMed:15339930};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:36340;
CC Evidence={ECO:0000269|PubMed:15339930};
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:0000269|PubMed:15339930};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:37064;
CC Evidence={ECO:0000269|PubMed:15339930};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01864,
CC ECO:0000269|PubMed:12766153, ECO:0000269|PubMed:17407324};
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, ECO:0000269|PubMed:12766153,
CC ECO:0000269|PubMed:17407324};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01864,
CC ECO:0000269|PubMed:12766153}.
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; AE000512; AAD35737.1; -; Genomic_DNA.
DR PIR; D72352; D72352.
DR RefSeq; NP_228462.1; NC_000853.1.
DR RefSeq; WP_004081141.1; NZ_CP011107.1.
DR AlphaFoldDB; Q9WZC1; -.
DR SMR; Q9WZC1; -.
DR STRING; 243274.THEMA_01400; -.
DR DNASU; 897761; -.
DR EnsemblBacteria; AAD35737; AAD35737; TM_0653.
DR KEGG; tma:TM0653; -.
DR eggNOG; COG0621; Bacteria.
DR InParanoid; Q9WZC1; -.
DR OMA; CEHFHIP; -.
DR OrthoDB; 397139at2; -.
DR BRENDA; 2.8.4.3; 6331.
DR Proteomes; UP000008183; 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..443
FT /note="tRNA-2-methylthio-N(6)-dimethylallyladenosine
FT synthase"
FT /id="PRO_0000359590"
FT DOMAIN 1..114
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT DOMAIN 136..367
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 370..431
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 10
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 46
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 79
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 150
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:0000305"
FT BINDING 154
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:0000305"
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:0000305"
FT MUTAGEN 10
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17407324"
FT MUTAGEN 150
FT /note="C->A: Decreased iron content and loss of activity;
FT when associated with A-154 and A-157."
FT /evidence="ECO:0000269|PubMed:17407324"
FT MUTAGEN 154
FT /note="C->A: Decreased iron content and loss of activity;
FT when associated with A-150 and A-157."
FT /evidence="ECO:0000269|PubMed:17407324"
FT MUTAGEN 157
FT /note="C->A: Decreased iron content and loss of activity;
FT when associated with A-150 and A-154."
FT /evidence="ECO:0000269|PubMed:17407324"
SQ SEQUENCE 443 AA; 50742 MW; 2C738B79667C9895 CRC64;
MRFYIKTFGC QMNENDSEAM AGLLVKEGFT PASSPEEADV VIINTCAVRR KSEEKAYSEL
GQVLKLKKKK KIVVGVAGCV AEKEREKFLE KGADFVLGTR AVPRVTEAVK KALEGEKVAL
FEDHLDEYTH ELPRIRTSRH HAWVTIIHGC DRFCTYCIVP YTRGRERSRP MADILEEVKK
LAEQGYREVT FLGQNVDAYG KDLKDGSSLA KLLEEASKIE GIERIWFLTS YPTDFSDELI
EVIAKNPKVA KSVHLPVQSG SNRILKLMNR RYTKEEYLAL LEKIRSKVPE VAISSDIIVG
FPTETEEDFM ETVDLVEKAQ FERLNLAIYS PREGTVAWKY YKDDVPYEEK VRRMQFLMNL
QKRINRKLNE RYRGKTVRII VEAQAKNGLF YGRDIRNKII AFEGEDWMIG RFADVKVEKI
TAGPLYGKVV WVEKTPSPVS SSE
