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Database: UniProt
Entry: R4Z7M9_9ACTN
LinkDB: R4Z7M9_9ACTN
Original site: R4Z7M9_9ACTN 
ID   R4Z7M9_9ACTN            Unreviewed;       499 AA.
AC   R4Z7M9;
DT   24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT   24-JUL-2013, sequence version 1.
DT   24-JAN-2024, entry version 50.
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   ECO:0000313|EMBL:CCM65787.1};
GN   ORFNames=BN381_80317 {ECO:0000313|EMBL:CCM65787.1};
OS   Candidatus Microthrix parvicella RN1.
OC   Bacteria; Actinomycetota; Acidimicrobiia; Acidimicrobiales;
OC   Microthrixaceae; Candidatus Microthrix.
OX   NCBI_TaxID=1229780 {ECO:0000313|EMBL:CCM65787.1, ECO:0000313|Proteomes:UP000018291};
RN   [1] {ECO:0000313|EMBL:CCM65787.1, ECO:0000313|Proteomes:UP000018291}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=RN1 {ECO:0000313|EMBL:CCM65787.1,
RC   ECO:0000313|Proteomes:UP000018291};
RX   PubMed=23446830; DOI=10.1038/ismej.2013.6;
RA   Jon McIlroy S., Kristiansen R., Albertsen M., Michael Karst S.,
RA   Rossetti S., Lund Nielsen J., Tandoi V., James Seviour R., Nielsen P.H.;
RT   "Metabolic model for the filamentous 'Candidatus Microthrix parvicella'
RT   based on genomic and metagenomic analyses.";
RL   ISME J. 7:1161-1172(2013).
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:CCM65787.1}.
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DR   EMBL; CANL01000078; CCM65787.1; -; Genomic_DNA.
DR   RefSeq; WP_012230837.1; NZ_HG422565.1.
DR   AlphaFoldDB; R4Z7M9; -.
DR   STRING; 1229780.BN381_80317; -.
DR   GeneID; 78312485; -.
DR   eggNOG; COG0621; Bacteria.
DR   HOGENOM; CLU_018697_2_2_11; -.
DR   OrthoDB; 9805215at2; -.
DR   Proteomes; UP000018291; 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; 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   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; PF00919; UPF0004; 1.
DR   SFLD; SFLDF00273; (dimethylallyl)adenosine_tRNA; 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:UP000018291};
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..119
FT                   /note="MTTase N-terminal"
FT                   /evidence="ECO:0000259|PROSITE:PS51449"
FT   DOMAIN          146..414
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000259|PROSITE:PS51918"
FT   DOMAIN          417..483
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         48
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         82
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         160
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"
FT   BINDING         167
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   499 AA;  54289 MW;  FF082CE3CCDE77D1 CRC64;
     MARKYLVRTF GCQMNEHDSE RIAGVLEADG LEATTEVSEA DVVVLNTCCI RENADNKLYG
     TLGHLKSEKD RRPELEIVVG GCLAQKDREV VQQRAPYVDV VMGTHNVGRV SELLEAARRD
     GPTMEILEAT AAADHEAFPS ALPAKREQGW AAWVTIQFGC DNSCAFCIVP AVRGPEISRP
     FGDVLDEVRR VAADGVTEVT LLGQNVDSYG RDLTLRVRGE HDGAPAGTPS HEFVVGEAWL
     TEREAMCASG RARPLFADLL RAVGSVPGIR RVRFTSPHPK DMRAETIAAM AHTAAVCEHL
     HLPMQSGSNE VLAAMHRGYT AERYLRVVHD ARIGIDDLAL TTDVIVGFPG ETEADFEATL
     EVCAEAQFDS AYTFIYSSRP GTEAAEMTAA FVDHAVSVNR MERLRAVIER SAVRANKARI
     GRVDEVVVTG PSRRDPSMIT GLTRHNKRIH LPAPAGVRPR PGTYVSALVT EARMTSLVGE
     IVDIGDSPVH RTRIPVSAG
//
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