ID F0ERE0_HAEPA Unreviewed; 436 AA.
AC F0ERE0;
DT 03-MAY-2011, integrated into UniProtKB/TrEMBL.
DT 03-MAY-2011, sequence version 1.
DT 27-MAR-2024, entry version 62.
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:EGC72996.1};
GN Synonyms=rlmD {ECO:0000256|HAMAP-Rule:MF_01010};
GN ORFNames=HMPREF9417_0518 {ECO:0000313|EMBL:EGC72996.1};
OS Haemophilus parainfluenzae ATCC 33392.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Haemophilus.
OX NCBI_TaxID=888828 {ECO:0000313|EMBL:EGC72996.1, ECO:0000313|Proteomes:UP000005577};
RN [1] {ECO:0000313|EMBL:EGC72996.1, ECO:0000313|Proteomes:UP000005577}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33392 {ECO:0000313|EMBL:EGC72996.1,
RC ECO:0000313|Proteomes:UP000005577};
RA Muzny D., Qin X., Deng J., Jiang H., Liu Y., Qu J., Song X.-Z., Zhang L.,
RA Thornton R., Coyle M., Francisco L., Jackson L., Javaid M., Korchina V.,
RA Kovar C., Mata R., Mathew T., Ngo R., Nguyen L., Nguyen N., Okwuonu G.,
RA Ongeri F., Pham C., Simmons D., Wilczek-Boney K., Hale W., Jakkamsetti A.,
RA Pham P., Ruth R., San Lucas F., Warren J., Zhang J., Zhao Z., Zhou C.,
RA Zhu D., Lee S., Bess C., Blankenburg K., Forbes L., Fu Q., Gubbala S.,
RA Hirani K., Jayaseelan J.C., Lara F., Munidasa M., Palculict T., Patil S.,
RA Pu L.-L., Saada N., Tang L., Weissenberger G., Zhu Y., Hemphill L.,
RA Shang Y., Youmans B., Ayvaz T., Ross M., Santibanez J., Aqrawi P.,
RA Gross S., Joshi V., Fowler G., Nazareth L., Reid J., Worley K.,
RA Petrosino J., Highlander S., Gibbs R.;
RL Submitted (JAN-2011) 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:EGC72996.1}.
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DR EMBL; AEWU01000008; EGC72996.1; -; Genomic_DNA.
DR RefSeq; WP_005695264.1; NZ_UGHU01000001.1.
DR AlphaFoldDB; F0ERE0; -.
DR GeneID; 67392148; -.
DR HOGENOM; CLU_014689_8_2_6; -.
DR Proteomes; UP000005577; 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; 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 15..64
FT /note="TRAM"
FT /evidence="ECO:0000259|Pfam:PF01938"
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 81
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 87
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 90
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 168
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 270
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 299
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 304
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT BINDING 320
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 436 AA; 49718 MW; FEAB5ACA9B4FBD92 CRC64;
MALLYAPQKK QKTTQKVVAE IQDLDYQGLG VSKIQGKTWF IENALPTEKV EAVVTDEKRQ
YGLAIAQKWL QKSSQRVEPQ CSYYERCGGC QGQHIPVEMQ RKAKEKALFS RLSKLQAEPI
QLMPMICGEQ WGYRRRVRLS LLWNAKNKTI EMGFRQKNSN QLVSIQQCLV AEPAINDLIP
KLTALWAQYS VPKQLGHVEL VSAENGVAML LRYKGNLAET DRTLLLEFAR VNAVNLFLQD
DQCIQLAHGE MPYYSLDDIR LSFDIRDFIQ VNTHLNLQMV ETALDWLDLN QDDHVLDLFC
GMGNFTLPLA KRVKSAVGIE GVFDMVQKAQ TNAQFNHIEN VEFYQADLDQ AFSEQPWAKQ
HFNKILLDPP RSGAAFALNA LCELCAEKIL YVSCNPATLV RDAEILRSFG YRIIKTAMID
MFPHTSHLES VTLFIK
//
