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RIMO_PARPJ
ID   RIMO_PARPJ              Reviewed;         461 AA.
AC   B2T3U5;
DT   26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-2008, sequence version 1.
DT   03-AUG-2022, entry version 80.
DE   RecName: Full=Ribosomal protein S12 methylthiotransferase RimO {ECO:0000255|HAMAP-Rule:MF_01865};
DE            Short=S12 MTTase {ECO:0000255|HAMAP-Rule:MF_01865};
DE            Short=S12 methylthiotransferase {ECO:0000255|HAMAP-Rule:MF_01865};
DE            EC=2.8.4.4 {ECO:0000255|HAMAP-Rule:MF_01865};
DE   AltName: Full=Ribosomal protein S12 (aspartate-C(3))-methylthiotransferase {ECO:0000255|HAMAP-Rule:MF_01865};
DE   AltName: Full=Ribosome maturation factor RimO {ECO:0000255|HAMAP-Rule:MF_01865};
GN   Name=rimO {ECO:0000255|HAMAP-Rule:MF_01865}; OrderedLocusNames=Bphyt_1848;
OS   Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN)
OS   (Burkholderia phytofirmans).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Paraburkholderia.
OX   NCBI_TaxID=398527;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 17436 / LMG 22146 / PsJN;
RX   PubMed=21551308; DOI=10.1128/jb.05055-11;
RA   Weilharter A., Mitter B., Shin M.V., Chain P.S., Nowak J., Sessitsch A.;
RT   "Complete genome sequence of the plant growth-promoting endophyte
RT   Burkholderia phytofirmans strain PsJN.";
RL   J. Bacteriol. 193:3383-3384(2011).
CC   -!- FUNCTION: Catalyzes the methylthiolation of an aspartic acid residue of
CC       ribosomal protein S12. {ECO:0000255|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:0000255|HAMAP-Rule:MF_01865};
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000255|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:0000255|HAMAP-Rule:MF_01865};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01865}.
CC   -!- SIMILARITY: Belongs to the methylthiotransferase family. RimO
CC       subfamily. {ECO:0000255|HAMAP-Rule:MF_01865}.
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DR   EMBL; CP001052; ACD16256.1; -; Genomic_DNA.
DR   RefSeq; WP_012432859.1; NC_010681.1.
DR   AlphaFoldDB; B2T3U5; -.
DR   SMR; B2T3U5; -.
DR   STRING; 398527.Bphyt_1848; -.
DR   EnsemblBacteria; ACD16256; ACD16256; Bphyt_1848.
DR   KEGG; bpy:Bphyt_1848; -.
DR   eggNOG; COG0621; Bacteria.
DR   HOGENOM; CLU_018697_0_0_4; -.
DR   OMA; HYAYPTG; -.
DR   OrthoDB; 397139at2; -.
DR   Proteomes; UP000001739; Chromosome 1.
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:0103039; F:protein methylthiotransferase activity; IEA:UniProtKB-EC.
DR   GO; GO:0018339; P:peptidyl-L-beta-methylthioaspartic acid biosynthetic process from peptidyl-aspartic acid; IEA:UniProtKB-UniRule.
DR   GO; GO:0006400; P:tRNA modification; IEA:InterPro.
DR   Gene3D; 2.40.50.140; -; 1.
DR   Gene3D; 3.40.50.12160; -; 1.
DR   Gene3D; 3.80.30.20; -; 1.
DR   HAMAP; MF_01865; MTTase_RimO; 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; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR005840; Ribosomal_S12_MeSTrfase_RimO.
DR   InterPro; IPR041582; RimO_TRAM.
DR   InterPro; IPR007197; rSAM.
DR   InterPro; IPR023404; rSAM_horseshoe.
DR   InterPro; IPR002792; TRAM_dom.
DR   PANTHER; PTHR43837; PTHR43837; 1.
DR   Pfam; PF04055; Radical_SAM; 1.
DR   Pfam; PF18693; TRAM_2; 1.
DR   Pfam; PF00919; UPF0004; 1.
DR   SFLD; SFLDS00029; Radical_SAM; 1.
DR   SFLD; SFLDF00274; ribosomal_protein_S12_methylth; 1.
DR   SMART; SM00729; Elp3; 1.
DR   TIGRFAMs; TIGR00089; TIGR00089; 1.
DR   TIGRFAMs; TIGR01125; TIGR01125; 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;
KW   S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..461
FT                   /note="Ribosomal protein S12 methylthiotransferase RimO"
FT                   /id="PRO_0000374740"
FT   DOMAIN          13..128
FT                   /note="MTTase N-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   DOMAIN          145..390
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   DOMAIN          393..461
FT                   /note="TRAM"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   BINDING         22
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   BINDING         58
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   BINDING         87
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   BINDING         159
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_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:0000255|HAMAP-Rule:MF_01865"
FT   BINDING         166
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_01865"
SQ   SEQUENCE   461 AA;  50210 MW;  B7248503B0C7B2B4 CRC64;
     MSATPPIVPT ATPKVGFVSL GCPKALVDSE QIITQLRAEG YEISGTYDGA DLVVVNTCGF
     IDEAVQESLD AIGEALNENG KVIVTGCLGA KKSASGSGLI EEVHPKVLAV TGPHALGEVM
     QHVHTHLPKP HDPFVDLVPA AGVKLTPRHY AYLKISEGCN HRCTFCIIPS MRGDLVSRPV
     ADVMLEAENL FKSGVKELLV ISQDTSAYGV DVKYRTGFWN GKPIKTRMTD LVGALGELAA
     QYGAWVRLHY VYPYPSVDEV IPMMAEGPYK GHVLPYLDVP FQHAHPEVLK RMKRPANAEK
     VMERVKKWRE MCPDLTIRST FIAGFPGETE EQFQTLLDFI REAELDRVGC FAYSPVEGAT
     ANELDGALPD EVREERRARF MEVAEEVSAK RIAKKVGKTL KVLVDEINAD GGIGRTAADA
     PEIDGVVYIA PAAKASKRYK VGDFVSVKIT GADGHDLWGE V
 
 
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