RLMD_HAES1
ID RLMD_HAES1 Reviewed; 439 AA.
AC Q0I127;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 87.
DE RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD {ECO:0000255|HAMAP-Rule:MF_01010};
DE EC=2.1.1.190 {ECO:0000255|HAMAP-Rule:MF_01010};
DE AltName: Full=23S rRNA(m5U1939)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01010};
GN Name=rlmD {ECO:0000255|HAMAP-Rule:MF_01010}; Synonyms=rumA;
GN OrderedLocusNames=HS_0094;
OS Haemophilus somnus (strain 129Pt) (Histophilus somni).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Histophilus.
OX NCBI_TaxID=205914;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=129Pt;
RX PubMed=17172329; DOI=10.1128/jb.01422-06;
RA Challacombe J.F., Duncan A.J., Brettin T.S., Bruce D., Chertkov O.,
RA Detter J.C., Han C.S., Misra M., Richardson P., Tapia R., Thayer N.,
RA Xie G., Inzana T.J.;
RT "Complete genome sequence of Haemophilus somnus (Histophilus somni) strain
RT 129Pt and comparison to Haemophilus ducreyi 35000HP and Haemophilus
RT influenzae Rd.";
RL J. Bacteriol. 189:1890-1898(2007).
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 1939
CC (m5U1939) in 23S rRNA. {ECO:0000255|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:0000255|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:0000255|HAMAP-Rule:MF_01010}.
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DR EMBL; CP000436; ABI24375.1; -; Genomic_DNA.
DR RefSeq; WP_011608249.1; NC_008309.1.
DR AlphaFoldDB; Q0I127; -.
DR SMR; Q0I127; -.
DR STRING; 205914.HS_0094; -.
DR PRIDE; Q0I127; -.
DR EnsemblBacteria; ABI24375; ABI24375; HS_0094.
DR KEGG; hso:HS_0094; -.
DR eggNOG; COG2265; Bacteria.
DR HOGENOM; CLU_014689_8_2_6; -.
DR OMA; FYAGDMK; -.
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 Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.150; -; 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 PANTHER; PTHR11061; PTHR11061; 1.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF53335; SSF53335; 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; Iron; Iron-sulfur; Metal-binding; Methyltransferase;
KW rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..439
FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT /id="PRO_0000282046"
FT DOMAIN 10..68
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT ACT_SITE 395
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 81
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 87
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 90
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 168
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 271
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 300
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 305
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 321
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 348
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 369
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ SEQUENCE 439 AA; 50884 MW; 0AC1656F66842EB8 CRC64;
MVLLYQPKKQ KKLRAAFTTI VQDLDYQGLG VAKIQGKTWF IENALPQEQV QVQVIEEKRQ
YGLGRVQKIL QASPLRQTPR CAYYQICGGC QSQHIPIHLQ RETKQKALFQ RLTKLQKEAI
EFMPMISGEA WHYRRRVRLS LYWDAKSKNL KIGFRQKNSQ QIVNIRQCDV LDPLLNELLP
KLHELLSTWS KPKTLGHIEL VAADNGVAML LRVTEKLAEH DRTLLLDFAF NHQVMLFVQD
EKEICHLQGD LPYYQLDDGS ILHFDIRDFI QVNRQLNQNM VNTALDWLDL KKKDNVLDLF
CGMGNFTLPI SRYVKSAVGI EGVLPMVEKA RRNGERNHCH NVQFYQCDLS QSFTEQEWAK
VPFDKILLDP PRSGAAFALN ALCYLMAEKI VYVSCNPATL VRDVELLLKF GYQLKKVAMI
DMFPHTSHLE SISLFERNR
