ID E0SEV7_DICD3 Unreviewed; 474 AA.
AC E0SEV7;
DT 02-NOV-2010, integrated into UniProtKB/TrEMBL.
DT 02-NOV-2010, sequence version 1.
DT 27-MAR-2024, entry version 84.
DE RecName: Full=tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase {ECO:0000256|ARBA:ARBA00033765, ECO:0000256|HAMAP-Rule:MF_01864};
DE EC=2.8.4.3 {ECO:0000256|ARBA:ARBA00033765, ECO:0000256|HAMAP-Rule:MF_01864};
DE AltName: Full=(Dimethylallyl)adenosine tRNA methylthiotransferase MiaB {ECO:0000256|HAMAP-Rule:MF_01864};
DE AltName: Full=tRNA-i(6)A37 methylthiotransferase {ECO:0000256|HAMAP-Rule:MF_01864};
GN Name=miaB {ECO:0000256|HAMAP-Rule:MF_01864,
GN ECO:0000313|EMBL:ADM97519.1};
GN OrderedLocusNames=Dda3937_02467 {ECO:0000313|EMBL:ADM97519.1};
OS Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937)).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Pectobacteriaceae; Dickeya.
OX NCBI_TaxID=198628 {ECO:0000313|EMBL:ADM97519.1, ECO:0000313|Proteomes:UP000006859};
RN [1] {ECO:0000313|EMBL:ADM97519.1, ECO:0000313|Proteomes:UP000006859}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=3937 {ECO:0000313|EMBL:ADM97519.1,
RC ECO:0000313|Proteomes:UP000006859};
RX PubMed=21217001; DOI=10.1128/JB.01513-10;
RA Glasner J.D., Yang C.H., Reverchon S., Hugouvieux-Cotte-Pattat N.,
RA Condemine G., Bohin J.P., Van Gijsegem F., Yang S., Franza T., Expert D.,
RA Plunkett G. III, San Francisco M.J., Charkowski A.O., Py B., Bell K.,
RA Rauscher L., Rodriguez-Palenzuela P., Toussaint A., Holeva M.C., He S.Y.,
RA Douet V., Boccara M., Blanco C., Toth I., Anderson B.D., Biehl B.S.,
RA Mau B., Flynn S.M., Barras F., Lindeberg M., Birch P.R., Tsuyumu S.,
RA Shi X., Hibbing M., Yap M.N., Carpentier M., Dassa E., Umehara M.,
RA Kim J.F., Rusch M., Soni P., Mayhew G.F., Fouts D.E., Gill S.R.,
RA Blattner F.R., Keen N.T., Perna N.T.;
RT "Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937.";
RL J. Bacteriol. 193:2076-2077(2011).
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:0000256|ARBA:ARBA00003234,
CC ECO:0000256|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:0000256|HAMAP-
CC Rule:MF_01864};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|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:0000256|HAMAP-Rule:MF_01864};
CC -!- SUBUNIT: Monomer. {ECO:0000256|HAMAP-Rule:MF_01864}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01864}.
CC -!- SIMILARITY: Belongs to the methylthiotransferase family. MiaB
CC subfamily. {ECO:0000256|HAMAP-Rule:MF_01864}.
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DR EMBL; CP002038; ADM97519.1; -; Genomic_DNA.
DR RefSeq; WP_013316982.1; NC_014500.1.
DR AlphaFoldDB; E0SEV7; -.
DR STRING; 198628.Dda3937_02467; -.
DR GeneID; 9732729; -.
DR KEGG; ddd:Dda3937_02467; -.
DR PATRIC; fig|198628.6.peg.1318; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_2_0_6; -.
DR OrthoDB; 9805215at2; -.
DR Proteomes; UP000006859; 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 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; SFLDG01061; methylthiotransferase; 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 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_01864};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01864};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_01864};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW Rule:MF_01864};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01864}; Reference proteome {ECO:0000313|Proteomes:UP000006859};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP-
KW Rule:MF_01864};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_01864}; tRNA processing {ECO:0000256|HAMAP-Rule:MF_01864}.
FT DOMAIN 3..120
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51449"
FT DOMAIN 143..375
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT DOMAIN 378..441
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT BINDING 12
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000256|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:0000256|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:0000256|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:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01864"
SQ SEQUENCE 474 AA; 53708 MW; 4DEC192BF7628BA7 CRC64;
MTKKLHIKTW GCQMNEYDSS KIADLLESTH GYQLTEVAEE ADILLLNTCS IREKAQEKVF
HQLGRWKTLK DVNPNLIIGV GGCVASQEGE HIRDRAHYVD VIFGPQTLHR LPEMINHVQG
TRSPIVDISF PEVEKFDRLP EPRAEGPTAF VSIMEGCNKY CTFCVVPYTR GEEVSRPVDD
VLFEIAQLAA QGVREVNLLG QNVNAYRGAT HNDDICSFAE LLRLVATIDG IDRIRFITSH
PIEFTDDIIS VYEDTPELVS FLHLPVQSGS DRVLTMMKRR HTALEYKAII RKLRNARPAI
QISSDFIVGF PGETQEDFEQ TMKLIADVDF DMSFSFIYSP RPGTPAADMV DDVTEAEKKQ
RLYILQERIN QQAMQYSRRM MGSVQRILVE GTSRKSVMEL SGRTENNRVV NFEGTPDMIG
KFVDVEIVDV YPNSLRGVVV RTEDQMDLRV SESPTSVIAR TRKENELGVG IYQP
//
