ID A0A257L479_9BACT Unreviewed; 470 AA.
AC A0A257L479;
DT 20-DEC-2017, integrated into UniProtKB/TrEMBL.
DT 20-DEC-2017, sequence version 1.
DT 27-MAR-2024, entry version 18.
DE SubName: Full=23S rRNA (Uracil(1939)-C(5))-methyltransferase RlmD {ECO:0000313|EMBL:OYU94447.1};
GN ORFNames=CFE21_15680 {ECO:0000313|EMBL:OYU94447.1};
OS Bacteroidetes bacterium B1(2017).
OC Bacteria; Bacteroidota.
OX NCBI_TaxID=2015582 {ECO:0000313|EMBL:OYU94447.1, ECO:0000313|Proteomes:UP000216329};
RN [1] {ECO:0000313|EMBL:OYU94447.1, ECO:0000313|Proteomes:UP000216329}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=B1 {ECO:0000313|EMBL:OYU94447.1};
RA Kojadinovic M., Villain A., Puppo C., Fon Sing S., Prioretti L., Hubert P.,
RA Gregori G., Zhang Y., Sassi J.-F., Claverie J.-M., Blanc G., Gontero B.;
RT "A metagenomic investigation of the 'star' freshwater diatom Asterionella
RT formosa and its bacterial cohort.";
RL Submitted (JUN-2017) to the EMBL/GenBank/DDBJ databases.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. {ECO:0000256|PROSITE-
CC ProRule:PRU01024}.
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:OYU94447.1}.
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DR EMBL; NKJG01000007; OYU94447.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A257L479; -.
DR Proteomes; UP000216329; Unassembled WGS sequence.
DR GO; GO:0008173; F:RNA methyltransferase activity; IEA:InterPro.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0034470; P:ncRNA processing; IEA:UniProt.
DR GO; GO:0009451; P:RNA modification; IEA:UniProt.
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 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 NCBIfam; TIGR00479; rumA; 1.
DR PANTHER; PTHR11061; RNA M5U METHYLTRANSFERASE; 1.
DR PANTHER; PTHR11061:SF30; TRNA (URACIL(54)-C(5))-METHYLTRANSFERASE; 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.
DR PROSITE; PS01231; TRMA_2; 1.
PE 3: Inferred from homology;
KW Methyltransferase {ECO:0000256|ARBA:ARBA00022603, ECO:0000256|PROSITE-
KW ProRule:PRU01024}; Reference proteome {ECO:0000313|Proteomes:UP000216329};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691,
KW ECO:0000256|PROSITE-ProRule:PRU01024};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|PROSITE-
KW ProRule:PRU01024}.
FT DOMAIN 1..64
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT ACT_SITE 428
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10015"
FT ACT_SITE 428
FT /note="Nucleophile"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 302
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 331
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 352
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 401
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01024"
SQ SEQUENCE 470 AA; 53774 MW; 2EC924576E36FFF4 CRC64;
MGKKKSKEPK FYENLHIVAA GSEGKSIARP EGMVVMLDYA VPGDIVNARV IQSKRRFEIA
TITEVVTPSE DRVPTFCEHF GTCGGCKWQQ MSYESQLRYK QQQVLDSFER IGKFPFPPME
PILGSAQTTH YRNKVEFSFT DRKWLTHATD IGTLSKAENA GLGYHIPGRF DKVFDMFTCH
LMAPLNDAIR NSVRDFCLEH DYDFFNLYGQ TGFMRNMTLR NNMRGEWMLI VSFGHEDKEK
REALLAHLHK NFPEIKALLY VINEKRNDTI FDLDIQVFAG DDFLIEELED LKFKIGPKSF
FQTNAYQTIE LYKKAREFAA LTGEELVYDL YTGVGTIALF VSKMAKKVVG IEYVEQAIED
AKKNAALNNI THTDFFAGDM KDLLTAEFMD LHGRPDVVIT DPPRAGMHED VIAQLLQVRP
KRIVYVSCNP ATQARDIALL TDVYEVKKVQ PVDMFPHTHH VENIALLELK
//
