ID D5WD20_PARAM Unreviewed; 461 AA. AC D5WD20; DT 13-JUL-2010, integrated into UniProtKB/TrEMBL. DT 13-JUL-2010, sequence version 1. DT 27-MAR-2024, entry version 80. 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 OrderedLocusNames=BC1002_2597 {ECO:0000313|EMBL:ADG16646.1}; OS Paraburkholderia atlantica. OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; OC Burkholderiaceae; Paraburkholderia. OX NCBI_TaxID=2654982 {ECO:0000313|EMBL:ADG16646.1, ECO:0000313|Proteomes:UP000002190}; RN [1] {ECO:0000313|EMBL:ADG16646.1, ECO:0000313|Proteomes:UP000002190} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=CCGE1002 {ECO:0000313|EMBL:ADG16646.1, RC ECO:0000313|Proteomes:UP000002190}; RG US DOE Joint Genome Institute; RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L., RA Pitluck S., Chertkov O., Detter J.C., Han C., Tapia R., Land M., Hauser L., RA Kyrpides N., Ovchinnikova G., Martinez-Romero E., Hernandez M.A.R., RA Tiedje J.M., Woyke T.; RT "Complete sequence of chromosome 1 of Burkholderia sp. CCGE1002."; RL Submitted (APR-2010) to the EMBL/GenBank/DDBJ databases. RN [2] {ECO:0000313|EMBL:ADG16646.1, ECO:0000313|Proteomes:UP000002190} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=CCGE1002 {ECO:0000313|EMBL:ADG16646.1, RC ECO:0000313|Proteomes:UP000002190}; RX PubMed=23209196; DOI=10.1128/JB.01756-12; RA Ormeno-Orrillo E., Rogel M.A., Chueire L.M., Tiedje J.M., RA Martinez-Romero E., Hungria M.; RT "Genome Sequences of Burkholderia sp. Strains CCGE1002 and H160, Isolated RT from Legume Nodules in Mexico and Brazil."; RL J. Bacteriol. 194:6927-6927(2012). 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; CP002013; ADG16646.1; -; Genomic_DNA. DR RefSeq; WP_013090486.1; NZ_JACHDG010000005.1. DR AlphaFoldDB; D5WD20; -. DR STRING; 640511.BC1002_2597; -. DR KEGG; bge:BC1002_2597; -. DR eggNOG; COG0621; Bacteria. DR HOGENOM; CLU_018697_2_0_4; -. DR Proteomes; UP000002190; Chromosome 1. 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|ARBA:ARBA00022490, 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}; 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}; KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP- KW Rule:MF_01864}. FT DOMAIN 3..120 FT /note="MTTase N-terminal" FT /evidence="ECO:0000259|PROSITE:PS51449" FT DOMAIN 143..381 FT /note="Radical SAM core" FT /evidence="ECO:0000259|PROSITE:PS51918" FT DOMAIN 384..451 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 461 AA; 51233 MW; DEC344B16A61E009 CRC64; MTKKVYVKTF GCQMNEYDSD KMVDVLGAAE GLVKTDTPED ADVILFNTCS VREKAQEKVF SDLGRVRELK DANPNLIIGV GGCVASQEGA SIVARAPYVD IVFGPQTLHR LPQMIDERRA SGRAQVDISF PEIEKFDHLP PARVEGPSAF VSIMEGCSKY CSYCVVPYTR GEEVSRPLDD VLTEIAGLAD QGVREVTLLG QNVNAYRGKF GGALTLGSTE IADFATLIEY VADIPGIERI RYTTSHPKEF TQRLIDTYAK VPKLVSHLHL PVQHGSDRIL MAMKRGYTVL EYKSVIRKLR AIRPDLSLST DMIVGFPGET EEDFAKMMAL VEEMKYDTSF SFIYSPRPGT PAANLHDDTP REVKLKRLQH LQATIEENVQ RISDAMVGNV ERILVERPAR KDPNELAGRT ENNRVVNFPA PVASHARLIG QMVDVKIVHA YPHSLRGELV MVRDDSTAAT H //