ID A0A0D6TP20_9FLAO Unreviewed; 482 AA.
AC A0A0D6TP20;
DT 27-MAY-2015, integrated into UniProtKB/TrEMBL.
DT 27-MAY-2015, sequence version 1.
DT 24-JAN-2024, entry version 40.
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=SY27_04300 {ECO:0000313|EMBL:KIX21911.1};
OS Flavobacterium sp. 316.
OC Bacteria; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC Flavobacteriaceae; Flavobacterium.
OX NCBI_TaxID=1603293 {ECO:0000313|EMBL:KIX21911.1, ECO:0000313|Proteomes:UP000032747};
RN [1] {ECO:0000313|EMBL:KIX21911.1, ECO:0000313|Proteomes:UP000032747}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=316 {ECO:0000313|EMBL:KIX21911.1,
RC ECO:0000313|Proteomes:UP000032747};
RA Karczewska-Golec J., Kochanowska-Lyzen M., Balut M., Golec P.,
RA Madanecki P., Markert S., Piotrowski A., Schweder T., Szalewska-Palasz A.;
RT "Three Bacterial Inhabitants of the Baltic Sea under Osmotic Stress: a
RT Genomic and a Proteomic Perspective.";
RL Submitted (FEB-2015) 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:KIX21911.1}.
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DR EMBL; JYGZ01000002; KIX21911.1; -; Genomic_DNA.
DR RefSeq; WP_045967590.1; NZ_JYGZ01000002.1.
DR AlphaFoldDB; A0A0D6TP20; -.
DR STRING; 1603293.SY27_04300; -.
DR PATRIC; fig|1603293.4.peg.875; -.
DR OrthoDB; 9805215at2; -.
DR Proteomes; UP000032747; 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; 2.40.50.140; Nucleic acid-binding proteins; 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; IPR012340; NA-bd_OB-fold.
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; SFLDF00413; CDK5RAP1; 1.
DR SFLD; SFLDS00029; Radical_SAM; 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:UP000032747};
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 24..140
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51449"
FT DOMAIN 164..410
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT DOMAIN 413..476
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT BINDING 33
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 69
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 103
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 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:0000256|HAMAP-Rule:MF_01864"
FT BINDING 182
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 185
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 482 AA; 55153 MW; FB5D5CEB324621D8 CRC64;
MEKIIEENKQ GTSLVLEQKE ENAKKLFIES YGCQMNFSDS EIVASILANQ GYNTTQNLEE
ADLVLVNTCS IRDKAEQTIR KRLEKYNAVK KINPNMKVGV LGCMAERLKD KFLEEEKIVD
MVVGPDAYKD IPNLLKEVED GRDAINVILS KEETYGDIAP VRLNSNGVTA FVSITRGCDN
MCTFCVVPFT RGRERSREPQ SIIEEIQDLW SRGFKEITLL GQNVDSYLWY GGGLKKDFVK
ATEMQKATSV DFAQLLDMCA SQFPKMRFRF STSNPQDMHV EVIEIMAKHH NICNYIHLPV
QSGSTRILNE MNRQHTREEY MTLIDNIKRI IPDISLSQDM ITGFPTETEE DHKDTLSLME
YVKYDFGFMF AYSERPGTMA ARKMEDDVPD EVKKRRLTEI VDLQQVHALE KTKRFVGQIV
EVLIEKDSKR SSEHWSGRNS QNTVVVFPKE NYKPGDFVNV KITDCTAATL IGEAVEYSTI
MQ
//