RIMO_NITEU
ID RIMO_NITEU Reviewed; 447 AA.
AC Q82VY8;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 111.
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=NE0911;
OS Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC
OS 14298).
OC Bacteria; Proteobacteria; Betaproteobacteria; Nitrosomonadales;
OC Nitrosomonadaceae; Nitrosomonas.
OX NCBI_TaxID=228410;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298;
RX PubMed=12700255; DOI=10.1128/jb.185.9.2759-2773.2003;
RA Chain P., Lamerdin J.E., Larimer F.W., Regala W., Lao V., Land M.L.,
RA Hauser L., Hooper A.B., Klotz M.G., Norton J., Sayavedra-Soto L.A.,
RA Arciero D.M., Hommes N.G., Whittaker M.M., Arp D.J.;
RT "Complete genome sequence of the ammonia-oxidizing bacterium and obligate
RT chemolithoautotroph Nitrosomonas europaea.";
RL J. Bacteriol. 185:2759-2773(2003).
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; AL954747; CAD84822.1; -; Genomic_DNA.
DR RefSeq; WP_011111522.1; NC_004757.1.
DR AlphaFoldDB; Q82VY8; -.
DR SMR; Q82VY8; -.
DR STRING; 228410.NE0911; -.
DR EnsemblBacteria; CAD84822; CAD84822; NE0911.
DR KEGG; neu:NE0911; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_0_0_4; -.
DR OMA; HYAYPTG; -.
DR OrthoDB; 397139at2; -.
DR PhylomeDB; Q82VY8; -.
DR Proteomes; UP000001416; 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..447
FT /note="Ribosomal protein S12 methylthiotransferase RimO"
FT /id="PRO_0000374902"
FT DOMAIN 15..125
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT DOMAIN 142..379
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 379..447
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT BINDING 24
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 60
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 89
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 156
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 160
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 163
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 447 AA; 49599 MW; 44DEDBCF1DA45AF9 CRC64;
MTSASSATIQ PPRIPRVGFV SLGCPKATVD SERILTCLRA EGYLISPSYA DADLVVVNTC
GFIDSAVAES LETIGEALTE NGKVIVTGCL GAKEDVIRQA HPSVLAVTGP QATEEVMQAI
HRHLPKPHDP YLDLVPPQGI KLTPKHYAYL KISEGCNHRC TFCIIPSMRG DLVSRPVGNV
LQEAQNLVDA GVRELLIISQ DTSAYGVDIK YRTGFWQGRP IRSRITELAR ALGELGIWIR
LHYVYPYPHV DELIPLMAEG KLLPYLDIPF QHGSKRILKL MKRPANSENV LARIRQWRDI
CPDIALRSTF IVGFPGETEQ EFEELLAFLE EAQLDRVGAF AYSPVKGAAA NALPDPVPSE
IQQERLARLM QWQEEISKKR LAGKKGRILK VLVDTVDENG VIARSYADAP EIDGVVYIEP
DFSIKPGDWV DVRITRTGIH DLWAKKI
