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Database: UniProt
Entry: A0A1I4QZX2_9BURK
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ID   A0A1I4QZX2_9BURK        Unreviewed;       465 AA.
AC   A0A1I4QZX2;
DT   22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT   22-NOV-2017, sequence version 1.
DT   24-JAN-2024, entry version 25.
DE   RecName: Full=Ribosomal protein uS12 methylthiotransferase RimO {ECO:0000256|HAMAP-Rule:MF_01865};
DE            Short=uS12 MTTase {ECO:0000256|HAMAP-Rule:MF_01865};
DE            Short=uS12 methylthiotransferase {ECO:0000256|HAMAP-Rule:MF_01865};
DE            EC=2.8.4.4 {ECO:0000256|HAMAP-Rule:MF_01865};
DE   AltName: Full=Ribosomal protein uS12 (aspartate-C(3))-methylthiotransferase {ECO:0000256|HAMAP-Rule:MF_01865};
DE   AltName: Full=Ribosome maturation factor RimO {ECO:0000256|HAMAP-Rule:MF_01865};
GN   Name=rimO {ECO:0000256|HAMAP-Rule:MF_01865};
GN   ORFNames=SAMN05444747_105288 {ECO:0000313|EMBL:SFM45622.1};
OS   Variovorax sp. OV329.
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC   Comamonadaceae; Variovorax.
OX   NCBI_TaxID=1882825 {ECO:0000313|EMBL:SFM45622.1, ECO:0000313|Proteomes:UP000199688};
RN   [1] {ECO:0000313|EMBL:SFM45622.1, ECO:0000313|Proteomes:UP000199688}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=OV329 {ECO:0000313|EMBL:SFM45622.1,
RC   ECO:0000313|Proteomes:UP000199688};
RA   de Groot N.N.;
RL   Submitted (OCT-2016) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Catalyzes the methylthiolation of an aspartic acid residue of
CC       ribosomal protein uS12. {ECO:0000256|HAMAP-Rule:MF_01865}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=[sulfur carrier]-SH + AH2 + L-aspartate(89)-[ribosomal protein
CC         uS12]-hydrogen + 2 S-adenosyl-L-methionine = 3-methylsulfanyl-L-
CC         aspartate(89)-[ribosomal protein uS12]-hydrogen + 5'-deoxyadenosine +
CC         [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-
CC         homocysteine; Xref=Rhea:RHEA:37087, Rhea:RHEA-COMP:10460, Rhea:RHEA-
CC         COMP:10461, Rhea:RHEA-COMP:14737, Rhea:RHEA-COMP:14739,
CC         ChEBI:CHEBI:13193, ChEBI:CHEBI:15378, ChEBI:CHEBI:17319,
CC         ChEBI:CHEBI:17499, ChEBI:CHEBI:29917, ChEBI:CHEBI:29961,
CC         ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:64428, ChEBI:CHEBI:73599; EC=2.8.4.4;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01865};
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01865};
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_01865};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01865}.
CC   -!- SIMILARITY: Belongs to the methylthiotransferase family. RimO
CC       subfamily. {ECO:0000256|HAMAP-Rule:MF_01865}.
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DR   EMBL; FOUG01000005; SFM45622.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A1I4QZX2; -.
DR   STRING; 1882825.SAMN05444747_105288; -.
DR   OrthoDB; 9805215at2; -.
DR   Proteomes; UP000199688; Unassembled WGS sequence.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005840; C:ribosome; IEA:UniProtKB-KW.
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:0103039; F:protein methylthiotransferase activity; IEA:UniProtKB-EC.
DR   GO; GO:0006400; P:tRNA modification; IEA:InterPro.
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_01865; MTTase_RimO; 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; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR005840; Ribosomal_uS12_MeSTrfase_RimO.
DR   InterPro; IPR007197; rSAM.
DR   InterPro; IPR023404; rSAM_horseshoe.
DR   InterPro; IPR002792; TRAM_dom.
DR   NCBIfam; TIGR01125; 30S ribosomal protein S12 methylthiotransferase RimO; 1.
DR   NCBIfam; TIGR00089; MiaB/RimO family radical SAM methylthiotransferase; 1.
DR   PANTHER; PTHR43837; RIBOSOMAL PROTEIN S12 METHYLTHIOTRANSFERASE RIMO; 1.
DR   PANTHER; PTHR43837:SF1; RIBOSOMAL PROTEIN S12 METHYLTHIOTRANSFERASE RIMO; 1.
DR   Pfam; PF04055; Radical_SAM; 1.
DR   Pfam; PF18693; TRAM_2; 1.
DR   Pfam; PF00919; UPF0004; 1.
DR   SFLD; SFLDG01082; B12-binding_domain_containing; 1.
DR   SFLD; SFLDG01061; methylthiotransferase; 1.
DR   SFLD; SFLDF00274; ribosomal_protein_S12_methylth; 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_01865};
KW   Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01865};
KW   Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_01865};
KW   Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW   Rule:MF_01865};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_01865}; Reference proteome {ECO:0000313|Proteomes:UP000199688};
KW   Ribonucleoprotein {ECO:0000313|EMBL:SFM45622.1};
KW   Ribosomal protein {ECO:0000313|EMBL:SFM45622.1};
KW   S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP-
KW   Rule:MF_01865};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW   Rule:MF_01865}.
FT   DOMAIN          17..132
FT                   /note="MTTase N-terminal"
FT                   /evidence="ECO:0000259|PROSITE:PS51449"
FT   DOMAIN          149..390
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000259|PROSITE:PS51918"
FT   DOMAIN          393..465
FT                   /note="TRAM"
FT                   /evidence="ECO:0000259|PROSITE:PS50926"
FT   BINDING         26
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01865"
FT   BINDING         62
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01865"
FT   BINDING         91
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01865"
FT   BINDING         163
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_01865"
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_01865"
FT   BINDING         170
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_01865"
SQ   SEQUENCE   465 AA;  50643 MW;  8B8C2CFAF1FC9FE7 CRC64;
     MAEAATPVRL ENPATAPKVG FVSLGCPKAL TDSELILTQL SAEGYQTSKT FEGADLVIVN
     TCGFIDDAVK ESLDTIGEAL AENGRVIVTG CLGAKSGDGG GNLVRQMHPS VLAVTGPHAT
     QEVMDAVHAN LPKPHDPFVD LVPPMGIKLT PKHYAYLKIS EGCNHRCTFC IIPSMRGDLV
     SRPIGDVLKE AKALFEGGVK ELLVISQDTS AYGVDVKYRT GFWDGTPVKT RMLELVRTLG
     EIAEPYGAWV RLHYVYPYPS VDEIIPLMAS GLVLPYLDVP LQHSHPAVLK RMKRPASGEK
     NLERIARWRE LCPELVIRST FIAGFPGETE EEFEHLLDFI REAGIDRAGC FAYSPVEGAT
     ANDIPGMLPE AEREARRSRF MEVAEEVSIA RLRRRIGATM QVLVDSAPAM GRKGGVGRSY
     ADAPEIDGIV RLLPPEKISK QLKVGEFTKA RVVDTQGHDL IALPI
//
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