RIMO_AKKM8
ID RIMO_AKKM8 Reviewed; 452 AA.
AC B2ULZ9;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 82.
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=Amuc_1623;
OS Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC
OS 81048 / CCUG 64013 / CIP 107961 / Muc).
OC Bacteria; Verrucomicrobia; Verrucomicrobiae; Verrucomicrobiales;
OC Akkermansiaceae; Akkermansia.
OX NCBI_TaxID=349741;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP
RC 107961 / Muc;
RX PubMed=21390229; DOI=10.1371/journal.pone.0016876;
RA van Passel M.W., Kant R., Zoetendal E.G., Plugge C.M., Derrien M.,
RA Malfatti S.A., Chain P.S., Woyke T., Palva A., de Vos W.M., Smidt H.;
RT "The genome of Akkermansia muciniphila, a dedicated intestinal mucin
RT degrader, and its use in exploring intestinal metagenomes.";
RL PLoS ONE 6:E16876-E16876(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}.
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DR EMBL; CP001071; ACD05443.1; -; Genomic_DNA.
DR RefSeq; WP_012420658.1; NC_010655.1.
DR AlphaFoldDB; B2ULZ9; -.
DR SMR; B2ULZ9; -.
DR STRING; 349741.Amuc_1623; -.
DR EnsemblBacteria; ACD05443; ACD05443; Amuc_1623.
DR KEGG; amu:Amuc_1623; -.
DR eggNOG; COG0621; Bacteria.
DR HOGENOM; CLU_018697_0_1_0; -.
DR OMA; HYAYPTG; -.
DR OrthoDB; 397139at2; -.
DR BioCyc; AMUC349741:G1GBX-1730-MON; -.
DR Proteomes; UP000001031; 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..452
FT /note="Ribosomal protein S12 methylthiotransferase RimO"
FT /id="PRO_0000374691"
FT DOMAIN 3..122
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT DOMAIN 148..392
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 395..452
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT BINDING 12
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 48
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 85
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 162
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 166
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 169
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 452 AA; 50864 MW; 7B96F8D1C49C1A0C CRC64;
MPLTVGLISL GCPKNLVDSE IMIGHLQKAG MTMTPEPELA DVMVVNTCAF IDQAKQEAID
AILDIVRARE NGAYPENQKL IVAGCLSQRF RKELPALLPE VDAFIGPDQI TKLPEIITQV
MDRTIQDRNF IEGKCRYVPD WNTPRYRLTP PHTAYIKIAE GCNHGCAYCI IPMIRGRHRS
RSQQDVVREA ETLIRSGVKE ICLIAQDITY YGMDKWTDAR PNRRSAVDSS RGESLASLLR
ALNAIEGEFW IRLLYTHPAH WSDELTAAIA ECPKVARYVD IPLQHISDNM LDAMQRVTDG
NYIRTLLRNI RKAVPGIAIR TTFITGFPGE TEDDHQELME FIEEFRFERA GIFTFSREEG
TKAYKMPNQV HHRTKARRYN EATLLLARLA SETGQEQIGR QIRVLVDAPG VARTEWDAPD
IDGTVSVPLT LPVGQFATVT VTDAVAYELT AE
