ID D3EPE6_ATETH Unreviewed; 439 AA.
AC D3EPE6;
DT 23-MAR-2010, integrated into UniProtKB/TrEMBL.
DT 23-MAR-2010, sequence version 1.
DT 27-MAR-2024, entry version 88.
DE RecName: Full=Ribosomal protein uS12 methylthiotransferase RimO {ECO:0000256|HAMAP-Rule:MF_01865};
DE Short=uS12 MTTase {ECO:0000256|HAMAP-Rule:MF_01865};
DE Short=uS12 methylthiotransferase {ECO:0000256|HAMAP-Rule:MF_01865};
DE EC=2.8.4.4 {ECO:0000256|HAMAP-Rule:MF_01865};
DE AltName: Full=Ribosomal protein uS12 (aspartate-C(3))-methylthiotransferase {ECO:0000256|HAMAP-Rule:MF_01865};
DE AltName: Full=Ribosome maturation factor RimO {ECO:0000256|HAMAP-Rule:MF_01865};
GN Name=rimO {ECO:0000256|HAMAP-Rule:MF_01865};
GN OrderedLocusNames=UCYN_06470 {ECO:0000313|EMBL:ADB95346.1};
OS Atelocyanobacterium thalassa (isolate ALOHA).
OC Bacteria; Cyanobacteriota; Cyanophyceae; Oscillatoriophycideae;
OC Chroococcales; Aphanothecaceae; Atelocyanobacterium;
OC Candidatus Atelocyanobacterium thalassa.
OX NCBI_TaxID=1453429 {ECO:0000313|Proteomes:UP000001405};
RN [1] {ECO:0000313|EMBL:ADB95346.1, ECO:0000313|Proteomes:UP000001405}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ALOHA {ECO:0000313|Proteomes:UP000001405};
RX PubMed=20173737; DOI=10.1038/nature08786;
RA Tripp H.J., Bench S.R., Turk K.A., Foster R.A., Desany B.A., Niazi F.,
RA Affourtit J.P., Zehr J.P.;
RT "Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium.";
RL Nature 464:90-94(2010).
CC -!- FUNCTION: Catalyzes the methylthiolation of an aspartic acid residue of
CC ribosomal protein uS12. {ECO:0000256|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:0000256|HAMAP-Rule:MF_01865};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|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:0000256|HAMAP-Rule:MF_01865};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01865}.
CC -!- SIMILARITY: Belongs to the methylthiotransferase family. RimO
CC subfamily. {ECO:0000256|HAMAP-Rule:MF_01865}.
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DR EMBL; CP001842; ADB95346.1; -; Genomic_DNA.
DR RefSeq; WP_012954033.1; NC_013771.1.
DR AlphaFoldDB; D3EPE6; -.
DR STRING; 1453429.UCYN_06470; -.
DR KEGG; cyu:UCYN_06470; -.
DR PATRIC; fig|713887.8.peg.603; -.
DR HOGENOM; CLU_018697_0_1_3; -.
DR OrthoDB; 9805215at2; -.
DR Proteomes; UP000001405; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005840; C:ribosome; IEA:UniProtKB-KW.
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:0006400; P:tRNA modification; IEA:InterPro.
DR CDD; cd01335; Radical_SAM; 1.
DR Gene3D; 3.40.50.12160; Methylthiotransferase, N-terminal domain; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR Gene3D; 3.80.30.20; tm_1862 like domain; 1.
DR HAMAP; MF_01865; MTTase_RimO; 1.
DR InterPro; IPR006638; Elp3/MiaA/NifB-like_rSAM.
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_uS12_MeSTrfase_RimO.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR023404; rSAM_horseshoe.
DR InterPro; IPR002792; TRAM_dom.
DR NCBIfam; TIGR01125; 30S ribosomal protein S12 methylthiotransferase RimO; 1.
DR NCBIfam; TIGR00089; MiaB/RimO family radical SAM methylthiotransferase; 1.
DR PANTHER; PTHR43837; RIBOSOMAL PROTEIN S12 METHYLTHIOTRANSFERASE RIMO; 1.
DR PANTHER; PTHR43837:SF1; RIBOSOMAL PROTEIN S12 METHYLTHIOTRANSFERASE RIMO; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF18693; TRAM_2; 1.
DR Pfam; PF00919; UPF0004; 1.
DR SFLD; SFLDG01082; B12-binding_domain_containing; 1.
DR SFLD; SFLDG01061; methylthiotransferase; 1.
DR SFLD; SFLDF00274; ribosomal_protein_S12_methylth; 1.
DR SMART; SM00729; Elp3; 1.
DR SUPFAM; SSF102114; Radical SAM enzymes; 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 {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_01865};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01865};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_01865};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW Rule:MF_01865};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01865}; Reference proteome {ECO:0000313|Proteomes:UP000001405};
KW Ribonucleoprotein {ECO:0000313|EMBL:ADB95346.1};
KW Ribosomal protein {ECO:0000313|EMBL:ADB95346.1};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP-
KW Rule:MF_01865};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_01865}.
FT DOMAIN 5..116
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51449"
FT DOMAIN 140..369
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT DOMAIN 372..438
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT BINDING 14
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01865"
FT BINDING 50
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01865"
FT BINDING 79
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000256|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:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01865"
SQ SEQUENCE 439 AA; 49502 MW; 80F80891D8518ADA CRC64;
MVKKPAIAIS HLGCEKNRID SEHILGLLAA EGYSVSSNEN LADYVVVNTC SFIQQAREES
VRTLVELAEN NKKIIIAGCM AQHFQDQLLE ELPEVVAIVG TGNYQEIVKT VQRVELGERV
IDISQKPTFI ADETVPRYRT TNEGVAYLRI AEGCNYRCTF CIIPHLRGNQ RSRTIESIVA
EAQQLANEGV QEIIIVSQIT TNYGLDLYGK VKLAELLQAL GKVNVPWIRV HYAYPTGLTA
EVLKAVKEVP NVIPYLDLPL QHSHPKILKA MNRPWKEAIN DEIIKSIRAS IPDVVLRTTF
IVGFPGETDE YFEHLVKFIK RHHFDHVGVF VFSPEEGTPS YKMPDQVPLE IAQERRDYLM
EIQQPISNRK NQQYVGKIVK VLIEQENTKT HQYIGRSIKS SPDVDGVVFV KGKAQLNSII
PVEITKADAY DLYGKVVQT
//
