RIMO_SYNWW
ID RIMO_SYNWW Reviewed; 439 AA.
AC Q0AXI3;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 95.
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=Swol_1262;
OS Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Syntrophomonadaceae;
OC Syntrophomonas.
OX NCBI_TaxID=335541;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 2245B / Goettingen;
RX PubMed=21966920; DOI=10.1111/j.1462-2920.2010.02237.x;
RA Sieber J.R., Sims D.R., Han C., Kim E., Lykidis A., Lapidus A.L.,
RA McDonnald E., Rohlin L., Culley D.E., Gunsalus R., McInerney M.J.;
RT "The genome of Syntrophomonas wolfei: new insights into syntrophic
RT metabolism and biohydrogen production.";
RL Environ. Microbiol. 12:2289-2301(2010).
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; CP000448; ABI68571.1; -; Genomic_DNA.
DR RefSeq; WP_011640673.1; NC_008346.1.
DR AlphaFoldDB; Q0AXI3; -.
DR SMR; Q0AXI3; -.
DR STRING; 335541.Swol_1262; -.
DR EnsemblBacteria; ABI68571; ABI68571; Swol_1262.
DR KEGG; swo:Swol_1262; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_0_1_9; -.
DR OMA; HYAYPTG; -.
DR OrthoDB; 397139at2; -.
DR Proteomes; UP000001968; 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 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.
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..439
FT /note="Ribosomal protein S12 methylthiotransferase RimO"
FT /id="PRO_0000375041"
FT DOMAIN 1..117
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT DOMAIN 140..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 10
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 46
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 80
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 154
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"
FT BINDING 161
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 439 AA; 49267 MW; 3D8F8B66D376F00B CRC64;
MNIGFISLGC SKNRVDTEVM MAALKKAGHR IVNSLERADL VVVNTCGFIT PAKEESIEAI
IETAELKKKG SLQFLIAAGC LSQRYGRELL LEIPELDGVF GISSVSSIAG VVNRIAQGER
VCFTEATPTE YFEKGHRILT TPPGSAYLKI SEGCNNSCSY CVIPSIRGKL RSRQINELLN
EAAQLLKMGI KELVLVAQDT SAYGHDISPQ SALPTLLREL SKLDGLEWIR LMYLHPLYLS
DDIIDVVAYE NKVLPYLDIP IQHASSKILK LMHRRHDNSH LRTMISKLRA RIPNLTLRTT
VMLGFPGEEE KDFAELYEFV AESQFDWLGA FSFVPEEGSK AALLPNQIED EIKAERKDKI
LRLQQKITRQ KNLARINTQE KVLISSQLSK NLFVGRTYFQ APEVDGLTLV KTDFKLTKGD
FVDVQLVGVR NYDMIGEYQ
