ID A0A1Y1SBV5_9GAMM Unreviewed; 438 AA.
AC A0A1Y1SBV5;
DT 30-AUG-2017, integrated into UniProtKB/TrEMBL.
DT 30-AUG-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=rumA {ECO:0000313|EMBL:ORE86130.1};
GN Synonyms=rlmD {ECO:0000256|HAMAP-Rule:MF_01010};
GN ORFNames=ATO7_12573 {ECO:0000313|EMBL:ORE86130.1};
OS Oceanococcus atlanticus.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales;
OC Ectothiorhodospiraceae; Oceanococcus.
OX NCBI_TaxID=1317117 {ECO:0000313|EMBL:ORE86130.1, ECO:0000313|Proteomes:UP000192342};
RN [1] {ECO:0000313|EMBL:ORE86130.1, ECO:0000313|Proteomes:UP000192342}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=22II-S10r2 {ECO:0000313|EMBL:ORE86130.1,
RC ECO:0000313|Proteomes:UP000192342};
RA Lai Q., Li G., Shao Z.;
RT "Oceanococcus atlanticus 22II-S10r2 Genome Sequencing.";
RL Submitted (APR-2013) 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:ORE86130.1}.
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DR EMBL; AQQV01000003; ORE86130.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1Y1SBV5; -.
DR STRING; 1317117.ATO7_12573; -.
DR OrthoDB; 9804590at2; -.
DR Proteomes; UP000192342; 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; 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:SF49; 23S RRNA (URACIL(1939)-C(5))-METHYLTRANSFERASE RLMD; 1.
DR PANTHER; PTHR11061; RNA M5U 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 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:UP000192342};
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..62
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT ACT_SITE 394
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10015"
FT ACT_SITE 394
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 75
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 81
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 84
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 163
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 271
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 300
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 BINDING 321
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 347
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 368
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 438 AA; 49285 MW; 8BE86C3CED2FC8B7 CRC64;
MSRKKVNREP RQGEVLDLTH DGRGVLRHEG KTVFVPDVLP GEAITYRAMR RKRSFDEGEL
LELHSRHADR VEPQCAHFGV CGGCVLQHLA PQSQLAFKQK HLADVFSRIG QVSPKRWLEP
LTGPHWGYRR RARLAVKYVH KKERVLVGFR ERGKPYVADI QRCEVLDPRV GHRLEELATL
IAGMDARESI PQIEVAMGDQ HVCLVFRHLE ALSNDDVERL RHYGRDTGLW IYLQPGGLDS
VHALEDDAPV LRYALPQYEV DLEFTPIDFV QVNAELNQRM IPHALALLDL QPEDRVLELF
AGLGNFTLPM ARAGARVIAV EGDDGLVERG RANANRQGLD AEYHVADLFQ PQQGAPWLQS
GFNKVLLDPP RAGAEQILPE LLAKKPQRIV YVSCHPASLA RDAGIIVNAG YRCSEAGVMD
MFPHTGHVES IALFERRS
//
