ID C6YX66_9GAMM Unreviewed; 449 AA.
AC C6YX66;
DT 22-SEP-2009, integrated into UniProtKB/TrEMBL.
DT 22-SEP-2009, sequence version 1.
DT 27-MAR-2024, entry version 70.
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:AJI74861.1};
GN Synonyms=rlmD {ECO:0000256|HAMAP-Rule:MF_01010};
GN ORFNames=BZ13_1850 {ECO:0000313|EMBL:AJI74861.1};
OS Francisella philomiragia subsp. philomiragia ATCC 25015.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Thiotrichales;
OC Francisellaceae; Francisella.
OX NCBI_TaxID=539329 {ECO:0000313|EMBL:AJI74861.1, ECO:0000313|Proteomes:UP000031897};
RN [1] {ECO:0000313|EMBL:AJI74861.1, ECO:0000313|Proteomes:UP000031897}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=O#319L {ECO:0000313|EMBL:AJI74861.1,
RC ECO:0000313|Proteomes:UP000031897};
RX PubMed=25931589;
RA Johnson S.L., Daligault H.E., Davenport K.W., Coyne S.R., Frey K.G.,
RA Koroleva G.I., Broomall S.M., Bishop-Lilly K.A., Bruce D.C., Chertkov O.,
RA Freitas T., Jaissle J., Ladner J.T., Rosenzweig C.N., Gibbons H.S.,
RA Palacios G.F., Redden C.L., Xu Y., Minogue T.D., Chain P.S.;
RT "Genome sequencing of 18 francisella strains to aid in assay development
RT and testing.";
RL Genome Announc. 3:0-0(2015).
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; CP010019; AJI74861.1; -; Genomic_DNA.
DR RefSeq; WP_004288123.1; NZ_DS999316.1.
DR AlphaFoldDB; C6YX66; -.
DR KEGG; fpt:BZ13_1850; -.
DR PATRIC; fig|539329.6.peg.1809; -.
DR HOGENOM; CLU_014689_8_2_6; -.
DR Proteomes; UP000031897; 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 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};
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..66
FT /note="TRAM"
FT /evidence="ECO:0000259|PROSITE:PS50926"
FT ACT_SITE 405
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10015"
FT ACT_SITE 405
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT ECO:0000256|PROSITE-ProRule:PRU01024"
FT BINDING 79
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 88
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 169
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 280
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 309
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 314
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 330
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 357
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 379
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 449 AA; 50951 MW; AB9ECB17B55D1169 CRC64;
MGRSRRHKKP QEGIFEAEII ALSHDGRGIA KVNGKTTFIP FTLPGEVVKF EYTFTKAKFD
EAKVVEYIKK SPNRVNPPCE YFEICGGCSL QHMSTDAQIE HKQQTLLNQL KYIGQGVEPQ
NILEPLRTTK TEGYRNKARL GVRYVNKKEK ILVGFRERNG RFLADIDSCK VLNPLVGEKL
TQIASFIETL SIYQHIAQLE IAIDDTRPAL IVRHLEPFVN EDLEKLKAFG LENGYWIYLQ
SKGPDTIFRL YPQEDVEPKK LSYQPVAGIN IGFEPNDFTQ VNNDINKKMI KRAIDLLEIS
ENDSIIDLFC GLGNFTLPIS QYAKTVIGVE GEQTMVGRAK ETAANNNISN VKFYAANLFE
SFEDKEWFNN FEYNKMLLDP PRAGAQEVCS NIEKFDVERI VYVSCDTATL ARDAGILVNH
KGYKLVSAGV MDMFPHTMHV ESIAVFEKV
//
