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RIMO_OPITP
ID   RIMO_OPITP              Reviewed;         471 AA.
AC   B1ZW93;
DT   26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   20-MAY-2008, sequence version 1.
DT   03-AUG-2022, entry version 79.
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=Oter_3568;
OS   Opitutus terrae (strain DSM 11246 / JCM 15787 / PB90-1).
OC   Bacteria; Verrucomicrobia; Opitutae; Opitutales; Opitutaceae; Opitutus.
OX   NCBI_TaxID=452637;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 11246 / JCM 15787 / PB90-1;
RX   PubMed=21398538; DOI=10.1128/jb.00228-11;
RA   van Passel M.W., Kant R., Palva A., Copeland A., Lucas S., Lapidus A.,
RA   Glavina del Rio T., Pitluck S., Goltsman E., Clum A., Sun H., Schmutz J.,
RA   Larimer F.W., Land M.L., Hauser L., Kyrpides N., Mikhailova N.,
RA   Richardson P.P., Janssen P.H., de Vos W.M., Smidt H.;
RT   "Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an
RT   abundant inhabitant of rice paddy soil ecosystems.";
RL   J. Bacteriol. 193:2367-2368(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; CP001032; ACB76845.1; -; Genomic_DNA.
DR   RefSeq; WP_012376374.1; NC_010571.1.
DR   AlphaFoldDB; B1ZW93; -.
DR   SMR; B1ZW93; -.
DR   STRING; 452637.Oter_3568; -.
DR   EnsemblBacteria; ACB76845; ACB76845; Oter_3568.
DR   KEGG; ote:Oter_3568; -.
DR   eggNOG; COG0621; Bacteria.
DR   HOGENOM; CLU_018697_0_1_0; -.
DR   OMA; HYAYPTG; -.
DR   OrthoDB; 397139at2; -.
DR   Proteomes; UP000007013; Chromosome.
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; Reference proteome;
KW   S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..471
FT                   /note="Ribosomal protein S12 methylthiotransferase RimO"
FT                   /id="PRO_0000374910"
FT   DOMAIN          2..122
FT                   /note="MTTase N-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   DOMAIN          152..395
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   DOMAIN          398..458
FT                   /note="TRAM"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   BINDING         11
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         47
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         84
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         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"
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:0000255|HAMAP-Rule:MF_01865"
FT   BINDING         173
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   471 AA;  52944 MW;  96C2F6DE211E7529 CRC64;
     MIKVSLISLG CAKNLVDSEI MVGHLHQAGM AVIPEAEKAD VVIVNTCSFI DSSKEESIGH
     ILEVHQHRGL RKRRKEQKLI VAGCMSQRFS KDLSSSLHDE VDAFIGLDQV TKVAPIIQEI
     YARERTKTDD PVSFVEGRST FIPDYDTPRF RLTPKHFAYV KIAEGCNHPC TFCIIPQIRG
     RHRSRTVESV VAEVRQLVRE GVKEINLISQ DTTFFGMDTW EQRPNPRTPV DSGRGTALTT
     LLRQLNAIEG DFWIRLLYTH PAHWSDELIR TIAECPKVAR YIDIPLQHIS DAMLSRMQRE
     TSGGYIRDLI ARIRAGIPGI AVRTTFIVGF PGETDADVDE LCAFISETKF ERLGVFRYSQ
     EDGTRAAKMP EQLSAKTKEA RWHRTMALQK QIAADVSKTY VGRTLRVLVE EPGVARGEAD
     APDIDGRVYV PRELPVGEFA DVTVTGYHDY DLLALPPGQK PAQWKVARQA Q
 
 
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