RLMCD_BACSU
ID RLMCD_BACSU Reviewed; 459 AA.
AC O31503;
DT 19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=23S rRNA (uracil-C(5))-methyltransferase RlmCD;
DE EC=2.1.1.189;
DE EC=2.1.1.190;
DE AltName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase;
DE AltName: Full=23S rRNA (uracil(747)-C(5))-methyltransferase;
GN Name=rlmCD; Synonyms=yefA, yerS; OrderedLocusNames=BSU06730;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND GENE NAME.
RC STRAIN=168;
RX PubMed=21824914; DOI=10.1093/nar/gkr626;
RA Desmolaize B., Fabret C., Bregeon D., Rose S., Grosjean H., Douthwaite S.;
RT "A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939
RT modifications in Bacillus subtilis 23S rRNA.";
RL Nucleic Acids Res. 39:9368-9375(2011).
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at positions 747
CC (m5U747) and 1939 (m5U1939) in 23S rRNA. {ECO:0000269|PubMed:21824914}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + uridine(747) in 23S rRNA = 5-
CC methyluridine(747) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42628, Rhea:RHEA-COMP:10154, Rhea:RHEA-COMP:10155,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.189;
CC Evidence={ECO:0000269|PubMed:21824914};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5-
CC methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42908, Rhea:RHEA-COMP:10278, Rhea:RHEA-COMP:10279,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.190;
CC Evidence={ECO:0000269|PubMed:21824914};
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01024}.
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DR EMBL; AL009126; CAB12493.1; -; Genomic_DNA.
DR PIR; E69793; E69793.
DR RefSeq; NP_388555.1; NC_000964.3.
DR RefSeq; WP_003233892.1; NZ_JNCM01000032.1.
DR AlphaFoldDB; O31503; -.
DR SMR; O31503; -.
DR STRING; 224308.BSU06730; -.
DR PaxDb; O31503; -.
DR PRIDE; O31503; -.
DR EnsemblBacteria; CAB12493; CAB12493; BSU_06730.
DR GeneID; 936060; -.
DR KEGG; bsu:BSU06730; -.
DR PATRIC; fig|224308.179.peg.731; -.
DR eggNOG; COG2265; Bacteria.
DR InParanoid; O31503; -.
DR OMA; FYAGDMK; -.
DR PhylomeDB; O31503; -.
DR BioCyc; BSUB:BSU06730-MON; -.
DR BRENDA; 2.1.1.189; 658.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0070475; P:rRNA base methylation; IBA:GO_Central.
DR GO; GO:0031167; P:rRNA methylation; IDA:UniProtKB.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR030390; MeTrfase_TrmA_AS.
DR InterPro; IPR030391; MeTrfase_TrmA_CS.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR002792; TRAM_dom.
DR InterPro; IPR010280; U5_MeTrfase_fam.
DR PANTHER; PTHR11061; PTHR11061; 1.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
DR PROSITE; PS50926; TRAM; 1.
DR PROSITE; PS01230; TRMA_1; 1.
DR PROSITE; PS01231; TRMA_2; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Methyltransferase;
KW Reference proteome; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..459
FT /note="23S rRNA (uracil-C(5))-methyltransferase RlmCD"
FT /id="PRO_0000161953"
FT DOMAIN 6..64
FT /note="TRAM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00208"
FT ACT_SITE 415
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 77
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 83
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 86
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 166
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 290
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 319
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 340
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 388
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
SQ SEQUENCE 459 AA; 51819 MW; 35E99547779421D5 CRC64;
MKMKPPVEKN EYYDVTFEDL THEGAGVAKV QGFPIFVPNA LPEEKAQIKV TRVKKGFAFG
RLIELKEESP HRTDAPCPIY KQCGGCQLQH MTYEGQLLFK QKQVKDVLER IGKLDLSKVT
VHPTLGMEDP WNYRNKAQVP VGEREGGLVA GFYQQRSHDI IDMSACLIQQ SKNDEAVQAV
KDICANYGVK AYNEERHKGW LRHIMVRYGV VTGEMMIVFI TRTSDFPHKA KIIEDITAQF
PHVKSIVQNI NPNKTNVIFG NETNVIWGEE YIYDLIGDVK FAISARSFYQ VNPEQTKVLY
DKALEYAELQ GEETVIDAYC GIGTISLFLA KQAKKVYGVE IVPEAIEDAK RNAELNGNTN
AEFAVGEAET VIPKWYEEGI TADTLVVDPP RKGCDEALLR TIVEMKPKRV VYVSCNPGTL
ARDLRVLEDG GYVTREVQPV DMFPHTNHVE CCVLIKLKE
