RLMD_STRMK
ID RLMD_STRMK Reviewed; 444 AA.
AC B2FPX2;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-JUN-2008, sequence version 1.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD {ECO:0000255|HAMAP-Rule:MF_01010};
DE EC=2.1.1.190 {ECO:0000255|HAMAP-Rule:MF_01010};
DE AltName: Full=23S rRNA(m5U1939)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01010};
GN Name=rlmD {ECO:0000255|HAMAP-Rule:MF_01010}; Synonyms=rumA;
GN OrderedLocusNames=Smlt3541;
OS Stenotrophomonas maltophilia (strain K279a).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Stenotrophomonas; Stenotrophomonas maltophilia group.
OX NCBI_TaxID=522373;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K279a;
RX PubMed=18419807; DOI=10.1186/gb-2008-9-4-r74;
RA Crossman L.C., Gould V.C., Dow J.M., Vernikos G.S., Okazaki A.,
RA Sebaihia M., Saunders D., Arrowsmith C., Carver T., Peters N., Adlem E.,
RA Kerhornou A., Lord A., Murphy L., Seeger K., Squares R., Rutter S.,
RA Quail M.A., Rajandream M.A., Harris D., Churcher C., Bentley S.D.,
RA Parkhill J., Thomson N.R., Avison M.B.;
RT "The complete genome, comparative and functional analysis of
RT Stenotrophomonas maltophilia reveals an organism heavily shielded by drug
RT resistance determinants.";
RL Genome Biol. 9:R74.1-R74.13(2008).
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 1939
CC (m5U1939) in 23S rRNA. {ECO:0000255|HAMAP-Rule:MF_01010}.
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:0000255|HAMAP-Rule:MF_01010};
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. RlmD subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01010}.
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DR EMBL; AM743169; CAQ46963.1; -; Genomic_DNA.
DR RefSeq; WP_005414201.1; NC_010943.1.
DR AlphaFoldDB; B2FPX2; -.
DR SMR; B2FPX2; -.
DR STRING; 522373.Smlt3541; -.
DR EnsemblBacteria; CAQ46963; CAQ46963; Smlt3541.
DR KEGG; sml:Smlt3541; -.
DR eggNOG; COG2265; Bacteria.
DR HOGENOM; CLU_014689_8_2_6; -.
DR OMA; FYAGDMK; -.
DR OrthoDB; 1421660at2; -.
DR Proteomes; UP000008840; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01010; 23SrRNA_methyltr_RlmD; 1.
DR InterPro; IPR001566; 23S_rRNA_MeTrfase_RlmD.
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; 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 3: Inferred from homology;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Methyltransferase;
KW Reference proteome; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..444
FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT /id="PRO_1000200857"
FT DOMAIN 5..67
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT ACT_SITE 400
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 80
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 86
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 89
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 168
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 276
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 305
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 310
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 326
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 353
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 374
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ SEQUENCE 444 AA; 49216 MW; 001A0BD6FF55C3C4 CRC64;
MARSRSRIDR TPFQTEILDL SHDGRGVARR EGEGGKVTFV SGALPGEVVM AEQTARSRHF
DEARTVEVLQ ASPQRVTPKC PHFGTCAGCV LQHLDEDQQI VAKQRVLMDN LERIGHVKPG
KVLAPLVGES WGYRRKGRFS VRRVEKKDKT LVGFREQDPR FVADLSQCLT VIPEIGTKVE
ALSTFIESLD GKRDIPQIEF IAGDQAVVLT VRHLQPLSDA DRAAWAAFGQ QHGFVIYLQS
GGVDTVQPLD GQGVPLSFRL APWDVELAFR PLDFIQVNAK LNEKMIAHAL DLLEPGEDER
VLDLFCGLGN FTLPLARRVR EVVGVEGDAG LVARARENAV RNGLANAQFF SADLTQDQRS
TPWMRQGFDK LLLDPPRSGA IEVLQQLPLK QFKRIVYVSC HPGSLARDAG YLVNEQGFTL
VSAGAMDMFP HTAHVESIAV FEKR
