RIMO_AFIC5
ID RIMO_AFIC5 Reviewed; 440 AA.
AC B6JF93; F8BTP6;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 16-DEC-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};
GN OrderedLocusNames=OCAR_6198, OCA5_c18330;
OS Afipia carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5)
OS (Oligotropha carboxidovorans).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Afipia.
OX NCBI_TaxID=504832;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49405 / DSM 1227 / KCTC 32145 / OM5;
RX PubMed=18539730; DOI=10.1128/jb.00614-08;
RA Paul D., Bridges S., Burgess S.C., Dandass Y., Lawrence M.L.;
RT "Genome sequence of the chemolithoautotrophic bacterium Oligotropha
RT carboxidovorans OM5T.";
RL J. Bacteriol. 190:5531-5532(2008).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49405 / DSM 1227 / KCTC 32145 / OM5;
RX PubMed=21742883; DOI=10.1128/jb.05619-11;
RA Volland S., Rachinger M., Strittmatter A., Daniel R., Gottschalk G.,
RA Meyer O.;
RT "Complete genome sequences of the chemolithoautotrophic Oligotropha
RT carboxidovorans strains OM4 and OM5.";
RL J. Bacteriol. 193:5043-5043(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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP001196; ACI93312.1; -; Genomic_DNA.
DR EMBL; CP002826; AEI06546.1; -; Genomic_DNA.
DR RefSeq; WP_012563338.1; NC_015684.1.
DR AlphaFoldDB; B6JF93; -.
DR SMR; B6JF93; -.
DR STRING; 504832.OCAR_6198; -.
DR EnsemblBacteria; AEI06546; AEI06546; OCA5_c18330.
DR KEGG; oca:OCAR_6198; -.
DR KEGG; ocg:OCA5_c18330; -.
DR PATRIC; fig|504832.7.peg.1956; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_0_0_5; -.
DR OMA; HYAYPTG; -.
DR OrthoDB; 397139at2; -.
DR Proteomes; UP000007730; 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..440
FT /note="Ribosomal protein S12 methylthiotransferase RimO"
FT /id="PRO_0000374909"
FT DOMAIN 7..117
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT DOMAIN 134..370
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 373..439
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT BINDING 16
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 52
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 81
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 148
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 152
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 155
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 440 AA; 48879 MW; 584E8428B9536C69 CRC64;
MNQGVPPKIS FVSLGCPKAL VDSERIITRL RAEGYELARK HDGADIVIVS TCGFLDSAKQ
ESLGAIGEAM AENGKVIVTG CMGAEPEQIE KEYPNLLSIT GPQQYESVLD AVHRALPPLH
NPHLDLLPPQ GIKLTPRHYA YLKISEGCNN RCTFCIIPKL RGDLVSRPAD DVLREAEKLV
VAGVKELLVV SQDTSAYGID IKYAPSAWKD REVRARFVDL ARELGELGAW VRLQYVYPYP
HVDDVIPLMG GNILPYLDIP FQHANTEVLK RMRRPAAQDK TLARIHKWRE QCPDLTLRST
FIVGFPGETE SEFQDLLDWL DEAQIDRLGC FKYEPVAGAT SNALENPVPD EIKTARWNAL
MARQQKISAQ RLKRKVGTRQ QVIIDEVGPS VAKGRSKADA PQIDGSVYVA SRRPLKVGDI
VTVKIERADE YDLHGSVAGF
