ID R6Y278_9FIRM Unreviewed; 478 AA.
AC R6Y278;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 24-JAN-2024, entry version 47.
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 ORFNames=BN617_00452 {ECO:0000313|EMBL:CDD22731.1};
OS Firmicutes bacterium CAG:345.
OC Bacteria; Bacillota.
OX NCBI_TaxID=1263020 {ECO:0000313|EMBL:CDD22731.1, ECO:0000313|Proteomes:UP000018232};
RN [1] {ECO:0000313|EMBL:CDD22731.1, ECO:0000313|Proteomes:UP000018232}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MGS:345 {ECO:0000313|Proteomes:UP000018232};
RA Nielsen H.B., Almeida M., Juncker A.S., Rasmussen S., Li J., Sunagawa S.,
RA Plichta D., Gautier L., Le Chatelier E., Peletier E., Bonde I., Nielsen T.,
RA Manichanh C., Arumugam M., Batto J., Santos M.B.Q.D., Blom N., Borruel N.,
RA Burgdorf K.S., Boumezbeur F., Casellas F., Dore J., Guarner F., Hansen T.,
RA Hildebrand F., Kaas R.S., Kennedy S., Kristiansen K., Kultima J.R.,
RA Leonard P., Levenez F., Lund O., Moumen B., Le Paslier D., Pons N.,
RA Pedersen O., Prifti E., Qin J., Raes J., Tap J., Tims S., Ussery D.W.,
RA Yamada T., MetaHit consortium, Renault P., Sicheritz-Ponten T., Bork P.,
RA Wang J., Brunak S., Ehrlich S.D.;
RT "Dependencies among metagenomic species, viruses, plasmids and units of
RT genetic variation.";
RL Submitted (NOV-2012) 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: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 -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:CDD22731.1}.
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DR EMBL; CBGR010000010; CDD22731.1; -; Genomic_DNA.
DR AlphaFoldDB; R6Y278; -.
DR STRING; 1263020.BN617_00452; -.
DR Proteomes; UP000018232; 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 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:UP000018232};
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 42..160
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51449"
FT DOMAIN 183..414
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT DOMAIN 416..478
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT BINDING 51
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 87
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 121
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 197
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 201
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 204
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 478 AA; 54308 MW; D600011C68A76472 CRC64;
MKDRSLSWPS LKAAGVRTKN KAQEISGLAK PSAFLLSWAA GRYFQVRTYG CQANVRDSEV
ITAYLQNLGM KPTTDPVQAD IIIFNTCAIR EHAETRIFGE LGHLAPLAKQ NYDLIIGLCG
CMAHEEVTLE KLRKNVKHLN LVFGTGNIHQ LYSLIEEQVK SKDRIFCVSS DNLPVVEEYP
EARFERYKAF VNIMYGCDKF CTYCIVPYTR GQQRSRNVED IVLEVKHLVE KGYKEVTLLG
QNVNAFGLDF EDKTKDFAYL LEQIAKTGIA RIRFTSPHPA DFKENVFKVM SEYKNIMPAL
HLPMQSGSSR VLKKMNRSYD RQRYLDLVKM LRSYIPDVRL TTDIICCFPG ETEEDFEDTL
SIIKEANFAG AYTFIYSPRN GTPAARWDNP LTPEEKQARF NRLASAIDEQ ATIAGNEAVG
QEVEVLFDSL DDKIGLIKGY DQYNRLVHVE APSTLIGQIK KVKILESHTY SFIGELLD
//
