RIMO_PSEE4
ID RIMO_PSEE4 Reviewed; 443 AA.
AC Q1I6D1;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2006, sequence version 1.
DT 03-AUG-2022, entry version 106.
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=PSEEN4113;
OS Pseudomonas entomophila (strain L48).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=384676;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=L48;
RX PubMed=16699499; DOI=10.1038/nbt1212;
RA Vodovar N., Vallenet D., Cruveiller S., Rouy Z., Barbe V., Acosta C.,
RA Cattolico L., Jubin C., Lajus A., Segurens B., Vacherie B., Wincker P.,
RA Weissenbach J., Lemaitre B., Medigue C., Boccard F.;
RT "Complete genome sequence of the entomopathogenic and metabolically
RT versatile soil bacterium Pseudomonas entomophila.";
RL Nat. Biotechnol. 24:673-679(2006).
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; CT573326; CAK16804.1; -; Genomic_DNA.
DR RefSeq; WP_011535175.1; NC_008027.1.
DR AlphaFoldDB; Q1I6D1; -.
DR SMR; Q1I6D1; -.
DR STRING; 384676.PSEEN4113; -.
DR EnsemblBacteria; CAK16804; CAK16804; PSEEN4113.
DR KEGG; pen:PSEEN4113; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_0_0_6; -.
DR OMA; HYAYPTG; -.
DR OrthoDB; 397139at2; -.
DR Proteomes; UP000000658; 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;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..443
FT /note="Ribosomal protein S12 methylthiotransferase RimO"
FT /id="PRO_0000374944"
FT DOMAIN 8..118
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT DOMAIN 137..375
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 378..443
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT BINDING 17
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 53
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 82
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 151
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"
FT BINDING 158
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 443 AA; 49408 MW; 55EF840663A08828 CRC64;
MSTTPATPKV GFVSLGCPKA LVDSERILTQ LRMEGYEVVP TYEDADVVVV NTCGFIDSAK
AESLEVIGEA IKENGKVIVT GCMGVEEGSI RDVHPSVLSV TGPQQYEQVV NAVHEVVPPR
QDHNPLIDLV PPQGVKLTPR HYAYLKISEG CNHSCSFCII PSMRGKLVSR PVGEVLSEAE
RLVKAGVKEI LVISQDTSAY GVDVKYKTDF WNGRPVKTRM LELCEALSSL GAWVRLHYVY
PYPNVDDVIP LMAAGKILPY LDIPFQHASP KVLKSMKRPA FEDRTLARIK NWREQCPELV
IRSTFIVGFP GETEEDFQYL LDWLTEAQLD RVGCFQYSPV EGAPANDLGL DEVPDDVKQE
RWDRFMAHQQ AISAARLQQR IGKEIEVLID EVEEQGSVGR SFFDAPEIDG SVFIDGDHGF
KPGDKVRCRI VDADEYDMWA EPI
