RIMO_THEMA
ID RIMO_THEMA Reviewed; 430 AA.
AC Q9X2H6;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 138.
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, ECO:0000269|PubMed:20007320, ECO:0000269|PubMed:23542644, ECO:0000269|PubMed:23991893};
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=TM_1862;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND REACTION MECHANISM.
RX PubMed=23991893; DOI=10.1021/ja4048448;
RA Landgraf B.J., Arcinas A.J., Lee K.H., Booker S.J.;
RT "Identification of an intermediate methyl carrier in the radical S-
RT adenosylmethionine methylthiotransferases RimO and MiaB.";
RL J. Am. Chem. Soc. 135:15404-15416(2013).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 135-430, CATALYTIC ACTIVITY,
RP COFACTOR, SUBUNIT, AND EPR SPECTROSCOPY.
RX PubMed=20007320; DOI=10.1074/jbc.m109.065516;
RA Arragain S., Garcia-Serres R., Blondin G., Douki T., Clemancey M.,
RA Latour J.M., Forouhar F., Neely H., Montelione G.T., Hunt J.F., Mulliez E.,
RA Fontecave M., Atta M.;
RT "Post-translational modification of ribosomal proteins: structural and
RT functional characterization of RimO from Thermotoga maritima, a radical S-
RT adenosylmethionine methylthiotransferase.";
RL J. Biol. Chem. 285:5792-5801(2010).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (3.30 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR CLUSTERS
RP CONNECTED VIA A PENTA-SULFIDE BRIDGE, COFACTOR, CATALYTIC ACTIVITY, AND EPR
RP SPECTROSCOPY.
RX PubMed=23542644; DOI=10.1038/nchembio.1229;
RA Forouhar F., Arragain S., Atta M., Gambarelli S., Mouesca J.M., Hussain M.,
RA Xiao R., Kieffer-Jaquinod S., Seetharaman J., Acton T.B., Montelione G.T.,
RA Mulliez E., Hunt J.F., Fontecave M.;
RT "Two Fe-S clusters catalyze sulfur insertion by radical-SAM
RT methylthiotransferases.";
RL Nat. Chem. Biol. 9:333-338(2013).
CC -!- FUNCTION: Catalyzes the methylthiolation of an aspartic acid residue of
CC ribosomal protein S12. {ECO:0000255|HAMAP-Rule:MF_01865,
CC ECO:0000269|PubMed:23991893}.
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 ECO:0000269|PubMed:20007320, ECO:0000269|PubMed:23542644,
CC ECO:0000269|PubMed:23991893};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01865,
CC ECO:0000269|PubMed:23542644};
CC Note=Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine. The two iron
CC atoms in each cluster are connected via a penta-sulfide bridge.
CC {ECO:0000255|HAMAP-Rule:MF_01865, ECO:0000269|PubMed:20007320,
CC ECO:0000269|PubMed:23542644};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:23542644}.
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; AE000512; AAD36924.1; -; Genomic_DNA.
DR PIR; G72201; G72201.
DR RefSeq; NP_229658.1; NC_000853.1.
DR RefSeq; WP_004082413.1; NZ_CP011107.1.
DR PDB; 2QGQ; X-ray; 2.00 A; A/B/C/D/E/F/G/H=135-430.
DR PDB; 4JC0; X-ray; 3.30 A; A/B=1-430.
DR PDBsum; 2QGQ; -.
DR PDBsum; 4JC0; -.
DR AlphaFoldDB; Q9X2H6; -.
DR SMR; Q9X2H6; -.
DR STRING; 243274.THEMA_04860; -.
DR EnsemblBacteria; AAD36924; AAD36924; TM_1862.
DR KEGG; tma:TM1862; -.
DR eggNOG; COG0621; Bacteria.
DR InParanoid; Q9X2H6; -.
DR OMA; HYAYPTG; -.
DR OrthoDB; 397139at2; -.
DR BRENDA; 2.8.4.4; 6331.
DR EvolutionaryTrace; Q9X2H6; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IBA:GO_Central.
DR GO; GO:0035599; F:aspartic acid methylthiotransferase activity; IBA:GO_Central.
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 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 3D-structure; 4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Metal-binding;
KW Reference proteome; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..430
FT /note="Ribosomal protein S12 methylthiotransferase RimO"
FT /id="PRO_0000375052"
FT DOMAIN 1..116
FT /note="MTTase N-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865"
FT DOMAIN 134..365
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT DOMAIN 367..430
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 ECO:0000269|PubMed:23542644"
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 ECO:0000269|PubMed:23542644"
FT BINDING 79
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01865,
FT ECO:0000269|PubMed:23542644"
FT BINDING 148
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 ECO:0000269|PubMed:23542644"
FT BINDING 152
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 ECO:0000269|PubMed:23542644"
FT BINDING 155
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 ECO:0000269|PubMed:23542644"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:4JC0"
FT HELIX 11..23
FT /evidence="ECO:0007829|PDB:4JC0"
FT TURN 24..26
FT /evidence="ECO:0007829|PDB:4JC0"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:4JC0"
FT STRAND 39..45
FT /evidence="ECO:0007829|PDB:4JC0"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:4JC0"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:4JC0"
FT HELIX 57..64
FT /evidence="ECO:0007829|PDB:4JC0"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:4JC0"
FT STRAND 73..78
FT /evidence="ECO:0007829|PDB:4JC0"
FT HELIX 79..82
FT /evidence="ECO:0007829|PDB:4JC0"
FT HELIX 85..91
FT /evidence="ECO:0007829|PDB:4JC0"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:4JC0"
FT TURN 104..107
FT /evidence="ECO:0007829|PDB:4JC0"
FT STRAND 138..145
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:4JC0"
FT HELIX 169..181
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 186..190
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 199..202
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 207..215
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 217..220
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 222..225
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 235..243
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 250..252
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 260..265
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 272..285
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 290..297
FT /evidence="ECO:0007829|PDB:2QGQ"
FT HELIX 304..317
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 320..326
FT /evidence="ECO:0007829|PDB:2QGQ"
FT TURN 334..337
FT /evidence="ECO:0007829|PDB:4JC0"
FT HELIX 344..367
FT /evidence="ECO:0007829|PDB:2QGQ"
FT TURN 368..371
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 373..382
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 385..390
FT /evidence="ECO:0007829|PDB:2QGQ"
FT TURN 395..397
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 401..405
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 412..421
FT /evidence="ECO:0007829|PDB:2QGQ"
FT STRAND 424..429
FT /evidence="ECO:0007829|PDB:2QGQ"
SQ SEQUENCE 430 AA; 49222 MW; 345477B796BF3990 CRC64;
MRVGIKVLGC PKNEADCEVL AGVLREGGHE IVFDVKDADV VVLDTCAFIE DAKRESIDEI
FSFVDAKDQY GYKLVVKGCL VQRYYEELKK EIPEVDQWIG VADPEEIANA IENGTDLVPD
QPETVYRYRK RIDLEERPYA YVKISDGCDR GCTFCSIPSF KGSLRSRSIE DITREVEDLL
KEGKKEIILV AQDTTSYGID LYRKQALPDL LRRLNSLNGE FWIRVMYLHP DHLTEEIISA
MLELDKVVKY FDVPVQHGSD KILKLMGRTK SSEELKKMLS SIRERFPDAV LRTSIIVGFP
GETEEDFEEL KQFVEEIQFD KLGAFVYSDE EGTVAFNLKE KVDPEMAKRR QEELLLLQAE
ISNSRLDRFV GKKLKFLVEG KEGKFLVGRT WTEAPEVDGV VFVRGKGKIG DFLEVVIKEH
DEYDMWGSVI
