MIAB_SHELP
ID MIAB_SHELP Reviewed; 474 AA.
AC A3QH41;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 17-APR-2007, sequence version 1.
DT 03-AUG-2022, entry version 94.
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=Shew_2923;
OS Shewanella loihica (strain ATCC BAA-1088 / PV-4).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=323850;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1088 / PV-4;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Mikhailova N., Romine M.F., Serres G.,
RA Fredrickson J., Tiedje J., Richardson P.;
RT "Complete sequence of Shewanella loihica PV-4.";
RL Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000606; ABO24789.1; -; Genomic_DNA.
DR RefSeq; WP_011866720.1; NC_009092.1.
DR AlphaFoldDB; A3QH41; -.
DR SMR; A3QH41; -.
DR STRING; 323850.Shew_2923; -.
DR EnsemblBacteria; ABO24789; ABO24789; Shew_2923.
DR KEGG; slo:Shew_2923; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_2_0_6; -.
DR OMA; CEHFHIP; -.
DR OrthoDB; 397139at2; -.
DR Proteomes; UP000001558; 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; 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; Reference proteome;
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_0000374540"
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 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; 53733 MW; F82E15EF92CE5062 CRC64;
MSKKLHIKTW GCQMNEYDSS KMADLLDEYQ GYTLTEEAEE ADVLLLNTCS IREKAQEKVF
HQLGRWKTLK DKNPNLIIGV GGCVASQEGK AIKDRAQCVD LIFGPQTLHR LPEMIEQIQQ
GGKAVIDVSF PEIEKFDRLP EPRAEGPSAF VSIMEGCSKY CSFCVVPYTR GEEVSRPVDD
VILEIAQLAE QGVREVNLLG QNVNAYRGAT HDDDICTFAE LLRYVAAIDG IDRIRFTTSH
PIEFTQDIID VYEDTPELVS FLHLPVQSGS DLILTQMKRG HMAIEYKSII RRLRKARPDI
QISSDFIVGF PGESKQDFAD TMKLIEDVQF DHSFSFIYSA RPGTPASDLP DDVSLDEKKE
RLAILQDRIT QQAMRYSRQM LGTVQRILVE GPSVKNPMEL RGRTENNRVV NFEADPKHIG
SFVDVEIVDV FTNSLRGKFI RGEDEMDLRR DLRPSDILAK HKKDDDLGVT QFIP
