RIMO_ECOLI
ID RIMO_ECOLI Reviewed; 441 AA.
AC P0AEI4; P75802;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Ribosomal protein S12 methylthiotransferase RimO;
DE Short=S12 MTTase;
DE Short=S12 methylthiotransferase;
DE EC=2.8.4.4 {ECO:0000269|PubMed:19736993};
DE AltName: Full=Ribosomal protein S12 (aspartate(89)-C(3))-methylthiotransferase;
DE AltName: Full=Ribosome maturation factor RimO;
GN Name=rimO; Synonyms=yliG; OrderedLocusNames=b0835, JW0819;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP FUNCTION AS A METHYLTHIOTRANSFERASE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=18252828; DOI=10.1073/pnas.0708608105;
RA Anton B.P., Saleh L., Benner J.S., Raleigh E.A., Kasif S., Roberts R.J.;
RT "RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88
RT residue of ribosomal protein S12 in Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:1826-1831(2008).
RN [5]
RP CATALYTIC ACTIVITY, COFACTOR, AND EPR SPECTROSCOPY.
RX PubMed=19736993; DOI=10.1021/bi900939w;
RA Lee K.H., Saleh L., Anton B.P., Madinger C.L., Benner J.S., Iwig D.F.,
RA Roberts R.J., Krebs C., Booker S.J.;
RT "Characterization of RimO, a new member of the methylthiotransferase
RT subclass of the radical SAM superfamily.";
RL Biochemistry 48:10162-10174(2009).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=21169565; DOI=10.1074/mcp.m110.005199;
RA Strader M.B., Costantino N., Elkins C.A., Chen C.Y., Patel I.,
RA Makusky A.J., Choy J.S., Court D.L., Markey S.P., Kowalak J.A.;
RT "A proteomic and transcriptomic approach reveals new insight into beta-
RT methylthiolation of Escherichia coli ribosomal protein S12.";
RL Mol. Cell. Proteomics 10:M110.005199.01-M110.005199.10(2011).
CC -!- FUNCTION: Catalyzes the methylthiolation of the residue Asp-89 of
CC ribosomal protein S12. {ECO:0000269|PubMed:18252828,
CC ECO:0000269|PubMed:21169565}.
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:0000269|PubMed:19736993};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:19736993};
CC Note=Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000269|PubMed:19736993};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Mutant shows a lack of methylthiolation of
CC protein S12 and a decrease in transcription of a subset of genes.
CC {ECO:0000269|PubMed:21169565}.
CC -!- SIMILARITY: Belongs to the methylthiotransferase family. RimO
CC subfamily. {ECO:0000305}.
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DR EMBL; U00096; AAC73922.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35530.1; -; Genomic_DNA.
DR PIR; C64821; C64821.
DR RefSeq; NP_415356.1; NC_000913.3.
DR RefSeq; WP_000049367.1; NZ_STEB01000019.1.
DR AlphaFoldDB; P0AEI4; -.
DR SMR; P0AEI4; -.
DR BioGRID; 4261845; 65.
DR BioGRID; 849839; 3.
DR DIP; DIP-48218N; -.
DR IntAct; P0AEI4; 20.
DR STRING; 511145.b0835; -.
DR jPOST; P0AEI4; -.
DR PaxDb; P0AEI4; -.
DR PRIDE; P0AEI4; -.
DR EnsemblBacteria; AAC73922; AAC73922; b0835.
DR EnsemblBacteria; BAA35530; BAA35530; BAA35530.
DR GeneID; 66670891; -.
DR GeneID; 945465; -.
DR KEGG; ecj:JW0819; -.
DR KEGG; eco:b0835; -.
DR PATRIC; fig|1411691.4.peg.1443; -.
DR EchoBASE; EB3251; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_0_0_6; -.
DR InParanoid; P0AEI4; -.
DR OMA; HYAYPTG; -.
DR PhylomeDB; P0AEI4; -.
DR BioCyc; EcoCyc:G6435-MON; -.
DR BioCyc; MetaCyc:G6435-MON; -.
DR BRENDA; 2.8.4.4; 2026.
DR PRO; PR:P0AEI4; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0035599; F:aspartic acid methylthiotransferase activity; IDA:EcoCyc.
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; IDA:EcoCyc.
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 1: Evidence at protein level;
KW 4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Metal-binding; Reference proteome;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..441
FT /note="Ribosomal protein S12 methylthiotransferase RimO"
FT /id="PRO_0000141738"
FT DOMAIN 8..118
FT /note="MTTase N-terminal"
FT DOMAIN 136..373
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 376..441
FT /note="TRAM"
FT BINDING 17
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 53
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 82
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
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:0000250"
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:0000250"
FT BINDING 157
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:0000250"
SQ SEQUENCE 441 AA; 49582 MW; E1D4605388AFB889 CRC64;
MSKVTPQPKI GFVSLGCPKN LVDSERILTE LRTEGYDVVP SYDDADMVIV NTCGFIDSAV
QESLEAIGEA LNENGKVIVT GCLGAKEDQI REVHPKVLEI TGPHSYEQVL EHVHHYVPKP
KHNPFLSLVP EQGVKLTPRH YAYLKISEGC NHRCTFCIIP SMRGDLVSRP IGEVLSEAKR
LVDAGVKEIL VISQDTSAYG VDVKHRTGFH NGEPVKTSMV SLCEQLSKLG IWTRLHYVYP
YPHVDDVIPL MAEGKILPYL DIPLQHASPR ILKLMKRPGS VDRQLARIKQ WREICPELTL
RSTFIVGFPG ETEEDFQMLL DFLKEARLDR VGCFKYSPVE GADANALPDQ VPEEVKEERW
NRFMQLQQQI SAERLQEKVG REILVIIDEV DEEGAIGRSM ADAPEIDGAV YLNGETNVKP
GDILRVKVEH ADEYDLWGSR V
