MIAB_STRV1
ID MIAB_STRV1 Reviewed; 505 AA.
AC D5ZT17;
DT 13-FEB-2019, integrated into UniProtKB/Swiss-Prot.
DT 13-JUL-2010, sequence version 1.
DT 03-AUG-2022, entry version 69.
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, ECO:0000303|PubMed:30543507};
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:30543507};
GN ORFNames=SSFG_01967 {ECO:0000312|EMBL:EFE66718.2};
OS Streptomyces viridosporus (strain ATCC 14672 / DSM 40746 / JCM 4963 / KCTC
OS 9882 / NRRL B-12104 / FH 1290) (Streptomyces ghanaensis).
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=566461;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 14672 / DSM 40746 / JCM 4963 / KCTC 9882 / NRRL B-12104 / FH
RC 1290;
RG The Broad Institute Genome Sequencing Platform;
RG Broad Institute Microbial Sequencing Center;
RA Fischbach M., Ward D., Young S., Kodira C.D., Zeng Q., Koehrsen M.,
RA Godfrey P., Alvarado L., Berlin A.M., Borenstein D., Chen Z., Engels R.,
RA Freedman E., Gellesch M., Goldberg J., Griggs A., Gujja S., Heiman D.I.,
RA Hepburn T.A., Howarth C., Jen D., Larson L., Lewis B., Mehta T., Park D.,
RA Pearson M., Roberts A., Saif S., Shea T.D., Shenoy N., Sisk P., Stolte C.,
RA Sykes S.N., Walk T., White J., Yandava C., Straight P., Clardy J., Hung D.,
RA Kolter R., Mekalanos J., Walker S., Walsh C.T., Wieland B.L.C., Ilzarbe M.,
RA Galagan J., Nusbaum C., Birren B.;
RT "Annotation of Streptomyces ghanaensis ATCC 14672.";
RL Submitted (DEC-2008) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 14672 / DSM 40746 / JCM 4963 / KCTC 9882 / NRRL B-12104 / FH
RC 1290;
RX PubMed=30543507; DOI=10.1099/mic.0.000747;
RA Sehin Y., Koshla O., Dacyuk Y., Zhao R., Ross R., Myronovskyi M.,
RA Limbach P.A., Luzhetskyy A., Walker S., Fedorenko V., Ostash B.;
RT "Gene ssfg_01967 (miaB) for tRNA modification influences morphogenesis and
RT moenomycin biosynthesis in Streptomyces ghanaensis ATCC14672.";
RL Microbiology 165:233-245(2019).
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 -!- DISRUPTION PHENOTYPE: Insertion mutant accumulates lower amounts of
CC moenomycin and is impaired in morphogenesis as compared to the parental
CC strain. Mutant shows reduced level of thiomethylation at position 37 in
CC the anticodon of tRNA. {ECO:0000269|PubMed:30543507}.
CC -!- SIMILARITY: Belongs to the methylthiotransferase family. MiaB
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01864}.
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DR EMBL; DS999641; EFE66718.2; -; Genomic_DNA.
DR RefSeq; WP_004982616.1; NZ_DS999641.1.
DR AlphaFoldDB; D5ZT17; -.
DR SMR; D5ZT17; -.
DR STRING; 566461.SSFG_01967; -.
DR EnsemblBacteria; EFE66718; EFE66718; SSFG_01967.
DR eggNOG; COG0621; Bacteria.
DR OMA; CEHFHIP; -.
DR OrthoDB; 397139at2; -.
DR Proteomes; UP000003824; Unassembled WGS sequence.
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..505
FT /note="tRNA-2-methylthio-N(6)-dimethylallyladenosine
FT synthase"
FT /id="PRO_0000446296"
FT DOMAIN 14..132
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT DOMAIN 155..386
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 388..456
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01864"
FT BINDING 23
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 61
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 95
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 169
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 173
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 176
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 505 AA; 55465 MW; BDFBF06679B518CC CRC64;
MSSIDRSQSV GGTRTYEVRT YGCQMNVHDS ERLAGLLEDA GYVRAPEGSD GDADVVVFNT
CAVRENADNK LYGNLGHLAP KKARRPGMQI AVGGCLAQKD RDTIVKRAPW VDVVFGTHNI
GKLPVLLERA RVQEEAQVEI AESLEAFPST LPTRRESAYA AWVSISVGCN NTCTFCIVPA
LRGKEKDRRP GDILAEIEAL VAEGVSEITL LGQNVNAYGS DIGDREAFSK LLRACGRIDG
LERVRFTSPH PRDFTDDVIA AMAETPNVMP QLHMPLQSGS DAVLKAMRRS YRQERYLGII
EKVRAAIPHA AISTDIIVGF PGETEEDFEQ TLHVVREARF AQAFTFQYSK RPGTPAAEMD
GQIPKKVVQE RYERLVALQE EISWEENKKQ VGRTLELMVA EGEGRKDDTT HRLSGRAPDN
RLVHFTKPEQ EVRPGDVVTV EITYAAPHHL LAEGPVRDVR RTRAGDAWEK RNAAEAAKPA
GVMLGLPKVG VPEPLPAVTG GCAVD
