ID A0A1J8P9X3_9COXI Unreviewed; 442 AA.
AC A0A1J8P9X3;
DT 15-FEB-2017, integrated into UniProtKB/TrEMBL.
DT 15-FEB-2017, sequence version 1.
DT 27-MAR-2024, entry version 26.
DE RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD {ECO:0000256|HAMAP-Rule:MF_01010};
DE EC=2.1.1.190 {ECO:0000256|HAMAP-Rule:MF_01010};
DE AltName: Full=23S rRNA(m5U1939)-methyltransferase {ECO:0000256|HAMAP-Rule:MF_01010};
GN Name=rlmD {ECO:0000256|HAMAP-Rule:MF_01010};
GN ORFNames=A1D18_04770 {ECO:0000313|EMBL:OIZ94175.1};
OS Candidatus Rickettsiella isopodorum.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Legionellales; Coxiellaceae;
OC Rickettsiella.
OX NCBI_TaxID=1225476 {ECO:0000313|EMBL:OIZ94175.1, ECO:0000313|Proteomes:UP000183924};
RN [1] {ECO:0000313|EMBL:OIZ94175.1, ECO:0000313|Proteomes:UP000183924}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RCFS May 2013 {ECO:0000313|EMBL:OIZ94175.1,
RC ECO:0000313|Proteomes:UP000183924};
RA Chandler C., Wang Y.;
RT "Comparative genomics of Rickettsiella.";
RL Submitted (MAR-2016) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 1939
CC (m5U1939) in 23S rRNA. {ECO:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01010}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:OIZ94175.1}.
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DR EMBL; LUKY01000033; OIZ94175.1; -; Genomic_DNA.
DR RefSeq; WP_071662668.1; NZ_LUKY01000033.1.
DR AlphaFoldDB; A0A1J8P9X3; -.
DR STRING; 1225476.A1D18_04770; -.
DR OrthoDB; 9804590at2; -.
DR Proteomes; UP000183924; Unassembled WGS sequence.
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 CDD; cd02440; AdoMet_MTases; 1.
DR Gene3D; 2.40.50.1070; -; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
DR HAMAP; MF_01010; 23SrRNA_methyltr_RlmD; 1.
DR InterPro; IPR001566; 23S_rRNA_MeTrfase_RlmD.
DR InterPro; IPR030390; MeTrfase_TrmA_AS.
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 NCBIfam; TIGR00479; rumA; 1.
DR PANTHER; PTHR11061:SF49; 23S RRNA (URACIL(1939)-C(5))-METHYLTRANSFERASE RLMD; 1.
DR PANTHER; PTHR11061; RNA M5U METHYLTRANSFERASE; 1.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
DR PROSITE; PS50926; TRAM; 1.
DR PROSITE; PS01230; TRMA_1; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_01010};
KW Iron {ECO:0000256|HAMAP-Rule:MF_01010};
KW Iron-sulfur {ECO:0000256|HAMAP-Rule:MF_01010};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_01010};
KW Methyltransferase {ECO:0000256|ARBA:ARBA00022603, ECO:0000256|HAMAP-
KW Rule:MF_01010}; Reference proteome {ECO:0000313|Proteomes:UP000183924};
KW rRNA processing {ECO:0000256|ARBA:ARBA00022552, ECO:0000256|HAMAP-
KW Rule:MF_01010};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP-
KW Rule:MF_01010};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_01010}.
FT DOMAIN 3..63
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT ACT_SITE 400
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10015"
FT ACT_SITE 400
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 76
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 82
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 85
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 164
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 276
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 305
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 310
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 326
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 353
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 374
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT ECO:0000256|PROSITE-ProRule:PRU01024"
SQ SEQUENCE 442 AA; 49940 MW; 867DE0129EF4C752 CRC64;
MENLKTSSIN TTPVVITGIS HEGRGIAHIN GKITFVENAL PGETVLIAYN KKRRSYDEAK
STQILKASTD RIQPECLHYD SCGGCSLQHL SNQAQLQHKE KTLTEQLIHF AEIKPKSLLP
PLKGASWGYR RRARLGVKYV TKKRAVLVGF REKNGRYLAQ LQTCKTLDPR VGQLLVPLQQ
LIHKLNAFQT IPQIEAALGD EMLGLVFRHL TPLDSSDQMQ LKNFAKQHKL QLYLQPGNES
TTHCIWPEDP KLLSYRLENK GYNPLELLFE PKHFVQINAN INQAMIQRAM ELLSPNFSDR
ILDLFCGLGN FSLPLATRCQ FVVGVEGYAE LVERAKANAR HNAINNTQFY TADLTGSILK
ETWIQQTFNK ILLDPPRSGA FEIIQQIAHW NVERIVYVSC NPASLARDAG ELIKQGYTLQ
QAGIMDMFPQ THHSEAICLF TK
//
