RLMD_RUBGI
ID RLMD_RUBGI Reviewed; 473 AA.
AC Q9JP88; I0HUI4;
DT 03-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 102.
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=RGE_33320;
OS Rubrivivax gelatinosus (strain NBRC 100245 / IL144).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Rubrivivax.
OX NCBI_TaxID=983917;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=NBRC 100245 / IL144;
RA Nagashima K.V., Igarashi N., Harada J., Nagashima S., Matsuura K.,
RA Shimada K.;
RL Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NBRC 100245 / IL144;
RX PubMed=22689232; DOI=10.1128/jb.00511-12;
RA Nagashima S., Kamimura A., Shimizu T., Nakamura-Isaki S., Aono E.,
RA Sakamoto K., Ichikawa N., Nakazawa H., Sekine M., Yamazaki S., Fujita N.,
RA Shimada K., Hanada S., Nagashima K.V.;
RT "Complete genome sequence of phototrophic betaproteobacterium Rubrivivax
RT gelatinosus IL144.";
RL J. Bacteriol. 194:3541-3542(2012).
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; AB034704; BAA94073.1; -; Genomic_DNA.
DR EMBL; AP012320; BAL96671.1; -; Genomic_DNA.
DR PIR; T50920; T50920.
DR RefSeq; WP_014429532.1; NC_017075.1.
DR AlphaFoldDB; Q9JP88; -.
DR SMR; Q9JP88; -.
DR STRING; 983917.RGE_33320; -.
DR EnsemblBacteria; BAL96671; BAL96671; RGE_33320.
DR KEGG; rge:RGE_33320; -.
DR PATRIC; fig|983917.3.peg.3255; -.
DR eggNOG; COG2265; Bacteria.
DR HOGENOM; CLU_014689_8_2_4; -.
DR OMA; FYAGDMK; -.
DR OrthoDB; 1421660at2; -.
DR Proteomes; UP000007883; 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; 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; 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..473
FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT /id="PRO_0000161911"
FT DOMAIN 1..58
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT ACT_SITE 403
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 71
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 81
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 84
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 163
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 271
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 300
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 321
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 349
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 370
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ SEQUENCE 473 AA; 51565 MW; 68D7787F480AC2F8 CRC64;
MSSGMDWLQV ESLDLEAQGV AHRADGKVVF IEGALPGETV QVQVSRRKNQ WEQGVLSALA
RESSQRVRPG CPHFGLHAGA CGGCKMQHLH PAAQVAVKQR VLEDNLWHLG KVKPERLLRP
IHGPAWGYRW RARLSVRYVP KKGVVLVGFH ERKSRYVADM LECPVLPAKV SAMLPALREL
IGAMEQRDRL PQIELAAGDE VIALVLRHLE PLSAGDAARL RAFGAEHGVQ WWLQPKGPET
VHRLDEGGPQ LAYSLPEYGV TMPFKPTDFT QVNPQINRVL VDRAVRLLAP QPHERIVDWF
CGLGNFTLPL ARRAAAVHGI EGSETLVQRA RENAAANGLA ANTSFAARNL FEMSADELMT
SGAADAWLVD PPREGAFALA KSLAELRGRE GWTPPRRIVY VSCNPATLAR DAGLIVHLAG
FRCVAAGVVN MFPHTAHVES IAVFERSEAA LSPRPVGEAA PELAAEPAPD AVA
