RLMD_ECOLI
ID RLMD_ECOLI Reviewed; 433 AA.
AC P55135; Q2MA47;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 167.
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, ygcA;
GN OrderedLocusNames=b2785, JW2756;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, AND
RP CHARACTERIZATION.
RX PubMed=11779873; DOI=10.1074/jbc.m111825200;
RA Agarwalla S., Kealey J.T., Santi D.V., Stroud R.M.;
RT "Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from
RT Escherichia coli.";
RL J. Biol. Chem. 277:8835-8840(2002).
RN [4]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=12907714; DOI=10.1093/nar/gkg657;
RA Madsen C.T., Mengel-Joergensen J., Kirpekar F., Douthwaite S.;
RT "Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA
RT using MALDI mass spectrometry.";
RL Nucleic Acids Res. 31:4738-4746(2003).
RN [5] {ECO:0007744|PDB:1UWV}
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 15-431, IRON-SULFUR CLUSTER, AND
RP DOMAIN.
RX PubMed=15016356; DOI=10.1016/j.str.2004.02.009;
RA Lee T.T., Agarwalla S., Stroud R.M.;
RT "Crystal structure of RumA, an iron-sulfur cluster containing E. coli
RT ribosomal RNA 5-methyluridine methyltransferase.";
RL Structure 12:397-407(2004).
RN [6] {ECO:0007744|PDB:2BH2}
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH RNA;
RP S-ADENOSYL-L-HOMOCYSTEINE AND IRON-SULFUR CLUSTER, AND ACTIVE SITE.
RX PubMed=15766524; DOI=10.1016/j.cell.2004.12.037;
RA Lee T.T., Agarwalla S., Stroud R.M.;
RT "A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to
RT substrate selectivity and enzymatic function.";
RL Cell 120:599-611(2005).
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 1939
CC (m5U1939) in 23S rRNA. {ECO:0000255|HAMAP-Rule:MF_01010,
CC ECO:0000269|PubMed:11779873, ECO:0000269|PubMed:12907714}.
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 ECO:0000269|PubMed:11779873, ECO:0000269|PubMed:12907714};
CC -!- DOMAIN: Contains three structural domains: an N-terminal TRAM domain, a
CC central domain containing an iron-sulfur cluster, and a C-terminal
CC domain that displays the typical SAM-dependent methyltransferase fold.
CC {ECO:0000269|PubMed:15016356}.
CC -!- MISCELLANEOUS: The function of the iron-sulfur cluster remains unclear.
CC It may be involved in the correct folding of the protein or may have a
CC role in RNA binding. {ECO:0000305|PubMed:15016356}.
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U29580; AAA69295.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75827.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76859.1; -; Genomic_DNA.
DR PIR; E65060; E65060.
DR RefSeq; NP_417265.1; NC_000913.3.
DR RefSeq; WP_000046812.1; NZ_STEB01000030.1.
DR PDB; 1UWV; X-ray; 1.95 A; A=1-433.
DR PDB; 2BH2; X-ray; 2.15 A; A/B=2-433.
DR PDBsum; 1UWV; -.
DR PDBsum; 2BH2; -.
DR AlphaFoldDB; P55135; -.
DR SMR; P55135; -.
DR BioGRID; 4262285; 70.
DR DIP; DIP-12119N; -.
DR IntAct; P55135; 2.
DR STRING; 511145.b2785; -.
DR jPOST; P55135; -.
DR PaxDb; P55135; -.
DR PRIDE; P55135; -.
DR EnsemblBacteria; AAC75827; AAC75827; b2785.
DR EnsemblBacteria; BAE76859; BAE76859; BAE76859.
DR GeneID; 947243; -.
DR KEGG; ecj:JW2756; -.
DR KEGG; eco:b2785; -.
DR PATRIC; fig|1411691.4.peg.3950; -.
DR EchoBASE; EB1228; -.
DR eggNOG; COG2265; Bacteria.
DR HOGENOM; CLU_014689_8_2_6; -.
DR InParanoid; P55135; -.
DR OMA; FYAGDMK; -.
DR PhylomeDB; P55135; -.
DR BioCyc; EcoCyc:EG11247-MON; -.
DR BioCyc; MetaCyc:EG11247-MON; -.
DR BRENDA; 2.1.1.190; 2026.
DR EvolutionaryTrace; P55135; -.
DR PRO; PR:P55135; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
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; IDA:EcoCyc.
DR GO; GO:0070475; P:rRNA base methylation; IDA:EcoCyc.
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 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Direct protein sequencing; Iron; Iron-sulfur;
KW Metal-binding; Methyltransferase; Reference proteome; rRNA processing;
KW S-adenosyl-L-methionine; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:11779873"
FT CHAIN 2..433
FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT /id="PRO_0000161893"
FT DOMAIN 10..68
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT REGION 23..40
FT /note="Interaction with RNA"
FT REGION 58..63
FT /note="Interaction with RNA"
FT ACT_SITE 389
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010,
FT ECO:0000269|PubMed:15766524"
FT BINDING 81
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:15016356,
FT ECO:0000269|PubMed:15766524"
FT BINDING 87
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:15016356,
FT ECO:0000269|PubMed:15766524"
FT BINDING 90
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:15016356,
FT ECO:0000269|PubMed:15766524"
FT BINDING 162
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:15016356,
FT ECO:0000269|PubMed:15766524"
FT BINDING 265
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:15766524"
FT BINDING 294
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:15766524"
FT BINDING 299
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:15766524"
FT BINDING 315
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:15766524"
FT BINDING 342
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:15766524"
FT BINDING 363
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:15766524"
FT SITE 132
FT /note="Interaction with RNA"
FT SITE 149
FT /note="Interaction with RNA"
FT STRAND 17..24
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 28..34
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 37..42
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 49..57
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 59..69
FT /evidence="ECO:0007829|PDB:1UWV"
FT TURN 82..86
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:2BH2"
FT HELIX 97..112
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 124..126
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 128..138
FT /evidence="ECO:0007829|PDB:1UWV"
FT TURN 139..142
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 143..150
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 167..180
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 184..188
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 189..197
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 200..209
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 213..226
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 229..237
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 240..243
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 248..251
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 254..257
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 268..282
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 289..294
FT /evidence="ECO:0007829|PDB:1UWV"
FT TURN 296..300
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 301..305
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 308..316
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 318..330
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 335..340
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 348..350
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 351..353
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 358..362
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 370..379
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 382..389
FT /evidence="ECO:0007829|PDB:1UWV"
FT HELIX 391..403
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 407..414
FT /evidence="ECO:0007829|PDB:1UWV"
FT STRAND 424..430
FT /evidence="ECO:0007829|PDB:1UWV"
SQ SEQUENCE 433 AA; 48052 MW; A46C07B0BD18EAAC CRC64;
MAQFYSAKRR TTTRQIITVS VNDLDSFGQG VARHNGKTLF IPGLLPQENA EVTVTEDKKQ
YARAKVVRRL SDSPERETPR CPHFGVCGGC QQQHASVDLQ QRSKSAALAR LMKHDVSEVI
ADVPWGYRRR ARLSLNYLPK TQQLQMGFRK AGSSDIVDVK QCPILAPQLE ALLPKVRACL
GSLQAMRHLG HVELVQATSG TLMILRHTAP LSSADREKLE RFSHSEGLDL YLAPDSEILE
TVSGEMPWYD SNGLRLTFSP RDFIQVNAGV NQKMVARALE WLDVQPEDRV LDLFCGMGNF
TLPLATQAAS VVGVEGVPAL VEKGQQNARL NGLQNVTFYH ENLEEDVTKQ PWAKNGFDKV
LLDPARAGAA GVMQQIIKLE PIRIVYVSCN PATLARDSEA LLKAGYTIAR LAMLDMFPHT
GHLESMVLFS RVK
