MIAB_CLAMS
ID MIAB_CLAMS Reviewed; 530 AA.
AC B0RGZ1;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 08-APR-2008, sequence version 1.
DT 03-AUG-2022, entry version 86.
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=CMS1210;
OS Clavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / DSM 20744
OS / JCM 9667 / LMG 2889 / C-1) (Corynebacterium sepedonicum).
OC Bacteria; Actinobacteria; Micrococcales; Microbacteriaceae; Clavibacter.
OX NCBI_TaxID=31964;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33113 / DSM 20744 / JCM 9667 / LMG 2889 / C-1;
RX PubMed=18192393; DOI=10.1128/jb.01598-07;
RA Bentley S.D., Corton C., Brown S.E., Barron A., Clark L., Doggett J.,
RA Harris B., Ormond D., Quail M.A., May G., Francis D., Knudson D.,
RA Parkhill J., Ishimaru C.A.;
RT "Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp.
RT sepedonicus suggests recent niche adaptation.";
RL J. Bacteriol. 190:2150-2160(2008).
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; AM849034; CAQ01325.1; -; Genomic_DNA.
DR RefSeq; WP_012298603.1; NZ_MZMN01000003.1.
DR AlphaFoldDB; B0RGZ1; -.
DR SMR; B0RGZ1; -.
DR STRING; 31964.CMS1210; -.
DR EnsemblBacteria; CAQ01325; CAQ01325; CMS1210.
DR KEGG; cms:CMS1210; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_2_2_11; -.
DR OMA; CEHFHIP; -.
DR Proteomes; UP000001318; 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; PF00919; UPF0004; 1.
DR SFLD; SFLDF00273; (dimethylallyl)adenosine_tRNA; 1.
DR SFLD; SFLDG01061; methylthiotransferase; 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..530
FT /note="tRNA-2-methylthio-N(6)-dimethylallyladenosine
FT synthase"
FT /id="PRO_0000374218"
FT DOMAIN 19..134
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT DOMAIN 157..387
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 390..460
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT REGION 509..530
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 28
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 63
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 97
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 171
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 175
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 178
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 530 AA; 57253 MW; C29F9F2F27111D82 CRC64;
MSTVAEHVRA APSSVDRPRT YEVRTYGCQM NVHDSERLTG SLEAAGYVSA EGAEADIVVI
NTCAVRENAD NKLYGNLGHL AGVKRRHEGM QIAVGGCLAQ KDRATVLEKA PWVDVVFGTH
NMGALPTLLE RARHNGEAQL EILESLETFP STLPTKRDEI ASGWVSISVG CNNTCTFCIV
PALRGKEKDR RPGDILAEIQ ALVDDGAVEV TLLGQNVNSY GVEFGDRQAF GKLLRAAGAI
EGLERIRFTS PHPAAFTDDV IDAMAETPAV MPQLHMPLQS GSDRILKAMR RSYRSERFLG
ILDRVRTRVP DAAITTDIIV GFPGETEEDF QETLRVVEAA RFSSAFTFQY SIRPGTPAAT
MEEQVPADVV KERYGRLTAL QERISHEENQ RVVGRTVEVL VSAHEGRKDG DTRRVTGRAQ
DGRLVHLDVP EGSAEPRPGD AVDVEVTRAA PFHLIADSVD GAPLRIRRTR AGDAWERAQA
DSCGVPTPAT GASAGAAPRV SLGLPTLRVP TTASTSAPVG DGSAHPRHRA
