ID A0A238T8Z8_9NEIS Unreviewed; 433 AA.
AC A0A238T8Z8;
DT 25-OCT-2017, integrated into UniProtKB/TrEMBL.
DT 25-OCT-2017, sequence version 1.
DT 27-MAR-2024, entry version 25.
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 ECO:0000313|EMBL:SNB51206.1};
GN ORFNames=KEBURONENSIS_00062 {ECO:0000313|EMBL:SNB51206.1};
OS Kingella negevensis.
OC Bacteria; Pseudomonadota; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Kingella.
OX NCBI_TaxID=1522312 {ECO:0000313|EMBL:SNB51206.1, ECO:0000313|Proteomes:UP000215450};
RN [1] {ECO:0000313|EMBL:SMQ11708.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Kingella_eburonensis {ECO:0000313|EMBL:SMQ11708.1};
RA Song R., Chenine A.L., Ruprecht R.M.;
RL Submitted (MAY-2017) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:SNB51206.1, ECO:0000313|Proteomes:UP000215450}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Kingella_eburonensis {ECO:0000313|EMBL:SNB51206.1};
RA Kim H.J., Triplett B.A.;
RL Submitted (JUN-2017) 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}.
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DR EMBL; FXUV01000001; SMQ11708.1; -; Genomic_DNA.
DR EMBL; FXUV02000001; SNB51206.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A238T8Z8; -.
DR STRING; 1522312.GCA_900177895_02131; -.
DR OrthoDB; 9804590at2; -.
DR Proteomes; UP000215450; 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; 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.
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:UP000215450};
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 1..53
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT ACT_SITE 389
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10015"
FT ACT_SITE 389
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 66
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 72
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 75
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 153
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 264
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 293
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 298
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 314
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 341
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 362
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 433 AA; 48119 MW; 4264CAC6B4FF1AE2 CRC64;
MNTAKIINID YEGRGVARLD GKTVFIHNAL PLETAEIQIT KDKGSFAEAE ATQILQASEY
RREPSCPHYG KCGGCALQHL EFSAQVAMKQ RIFEEQLQRI GKVQPENLLP PIYGAKWHYR
SRTRLSIFVD KQGRVNIGYQ AKRSKRIVPI SQCAVLPEHV SGSLKTIRDG LQQIHEAAPK
VRLESVEISV GDEITVLNII ADKSLPENVL AQFSGSLKMG NWQIWQQIGK RAAQAVAPKN
APELSYRLPE FGLRMPFRVG DFTQINLPMN EVMVSRALRL LQPQAHERIA DLFCGLGNFT
LPIARSGAQV VGIEGADFLT KRAMNNAKAN GLANIEFSTA DLFDTTPQTI ERLGYFDKML
LDPPRAGAYA VVQALHAPFL PKRIVYVSCN PATFARDATV LVEKGYRFRE AGVMNLFPHT
AHIEAVAVFD LEA
//
