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RIMO_CHLT3
ID   RIMO_CHLT3              Reviewed;         434 AA.
AC   B3QSS3;
DT   26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   02-SEP-2008, sequence version 1.
DT   03-AUG-2022, entry version 78.
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=Ctha_1662;
OS   Chloroherpeton thalassium (strain ATCC 35110 / GB-78).
OC   Bacteria; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chloroherpeton.
OX   NCBI_TaxID=517418;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 35110 / GB-78;
RG   US DOE Joint Genome Institute;
RA   Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA   Bruce D., Goodwin L., Pitluck S., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Kyrpides N., Mikhailova N., Liu Z., Li T., Zhao F., Overmann J.,
RA   Bryant D.A., Richardson P.;
RT   "Complete sequence of Chloroherpeton thalassium ATCC 35110.";
RL   Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases.
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; CP001100; ACF14120.1; -; Genomic_DNA.
DR   RefSeq; WP_012500204.1; NC_011026.1.
DR   AlphaFoldDB; B3QSS3; -.
DR   SMR; B3QSS3; -.
DR   STRING; 517418.Ctha_1662; -.
DR   EnsemblBacteria; ACF14120; ACF14120; Ctha_1662.
DR   KEGG; cts:Ctha_1662; -.
DR   eggNOG; COG0621; Bacteria.
DR   HOGENOM; CLU_018697_0_1_10; -.
DR   OMA; HYAYPTG; -.
DR   OrthoDB; 397139at2; -.
DR   Proteomes; UP000001208; 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; SFLDG01061; methylthiotransferase; 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..434
FT                   /note="Ribosomal protein S12 methylthiotransferase RimO"
FT                   /id="PRO_0000374771"
FT   DOMAIN          6..122
FT                   /note="MTTase N-terminal"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   DOMAIN          132..361
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   DOMAIN          364..434
FT                   /note="TRAM"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT   BINDING         15
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         51
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         85
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         146
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         150
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         153
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   434 AA;  49883 MW;  1459968E9F8E2D75 CRC64;
     METKRSKLYL LTLGCSKNMV DSEVLLAQAK ANQIYLAEDF HEADTILINT CGFIDKSKQE
     SIDQILEAIR FKEAKRIKKV IVFGCLSERY KDALREEIPE VDCYFGTRDL SQIIAELGGH
     YKTHLLGERE LLTPPYFSYL KISEGCDHPC AFCAIPLMRG KQVSRPIDEL LLEAKKLKEK
     GVRELCLIAQ DTTYYGHDLN GKRQLAELLQ RLSDLQFDWI RLLYAYPAMF PTDILPVMRE
     RENICKYLDL PLQHVSDEML KSMRRGISKR KTTELIAQIR SEVPGIRLRT TMLVGYPNET
     EEQFSELVEF VRETQFDRLG CFAYSHEEGT EAHELPDTLT EEEKERRVEL LMAAQEEIAY
     AKNQALVGSF MPVLIERFEA NFAIGRTEYD APEVDNEVVI ALDEAEQKKV KVGTFYQARI
     TDAEAFDLFG SLVL
 
 
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