RLMM_ECOLI
ID RLMM_ECOLI Reviewed; 366 AA.
AC P0ADR6; P32066; Q2MA28;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Ribosomal RNA large subunit methyltransferase M;
DE EC=2.1.1.186;
DE AltName: Full=23S rRNA (cytidine2498-2'-O)-methyltransferase;
DE AltName: Full=23S rRNA 2'-O-ribose methyltransferase RlmM;
GN Name=rlmM; Synonyms=ygdE; OrderedLocusNames=b2806, JW2777; ORFNames=b1976;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=7704273; DOI=10.1099/13500872-141-2-419;
RA Everett M.J., Walsh T., Guay G., Bennett P.M.;
RT "GcvA, a LysR-type transcriptional regulator protein, activates expression
RT of the cloned Citrobacter freundii ampC beta-lactamase gene in Escherichia
RT coli: cross-talk between DNA-binding proteins.";
RL Microbiology 141:419-430(1995).
RN [2]
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 [3]
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 [4]
RP PUTATIVE FUNCTION AS METHYLTRANSFERASE.
RX PubMed=11293658;
RA Bujnicki J.M., Rychlewski L.;
RT "Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded
RT by the Escherichia coli YgdE open reading frame and its orthologs.";
RL Acta Microbiol. Pol. 49:253-260(2000).
RN [5]
RP PUTATIVE FUNCTION AS METHYLTRANSFERASE.
RX PubMed=12527203; DOI=10.1016/s0378-1119(02)01097-1;
RA Feder M., Pas J., Wyrwicz L.S., Bujnicki J.M.;
RT "Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-
RT O-methyltransferases.";
RL Gene 302:129-138(2003).
RN [6]
RP FUNCTION AS A METHYLTRANSFERASE, AND CATALYTIC ACTIVITY.
RX PubMed=19400805; DOI=10.1111/j.1365-2958.2009.06709.x;
RA Purta E., O'Connor M., Bujnicki J.M., Douthwaite S.;
RT "YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide
RT C2498 in bacterial 23S rRNA.";
RL Mol. Microbiol. 72:1147-1158(2009).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOPENZYME AND IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, DOMAIN,
RP AND SUBUNIT.
RX PubMed=22923526; DOI=10.1093/nar/gks727;
RA Punekar A.S., Shepherd T.R., Liljeruhm J., Forster A.C., Selmer M.;
RT "Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of
RT Escherichia coli 23S rRNA.";
RL Nucleic Acids Res. 40:10507-10520(2012).
CC -!- FUNCTION: Catalyzes the 2'-O-methylation at nucleotide C2498 in 23S
CC rRNA. Modifies C2498 in naked 23S rRNA, but not in assembled 50S
CC subunits or ribosomes. {ECO:0000269|PubMed:19400805,
CC ECO:0000269|PubMed:22923526}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(2498) in 23S rRNA + S-adenosyl-L-methionine = 2'-O-
CC methylcytidine(2498) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42788, Rhea:RHEA-COMP:10244, Rhea:RHEA-COMP:10245,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.186;
CC Evidence={ECO:0000269|PubMed:19400805, ECO:0000269|PubMed:22923526};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:22923526}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DOMAIN: Consists of two structural domains: an N-terminal THUMP domain
CC followed by a C-terminal catalytic Rossmann-like fold MTase domain in a
CC novel arrangement. The two domains are connected by a long loop.
CC {ECO:0000269|PubMed:22923526}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA methyltransferase RlmE family. RlmM subfamily.
CC {ECO:0000305}.
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; X73413; CAA51815.1; -; Genomic_DNA.
DR EMBL; U29581; AAB40456.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75848.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76878.1; -; Genomic_DNA.
DR PIR; I41067; I41067.
DR RefSeq; NP_417286.1; NC_000913.3.
DR RefSeq; WP_001045520.1; NZ_STEB01000030.1.
DR PDB; 4ATN; X-ray; 1.95 A; A=1-366.
DR PDB; 4AUK; X-ray; 1.90 A; A/B=1-366.
DR PDB; 4B17; X-ray; 2.60 A; A=1-366.
DR PDBsum; 4ATN; -.
DR PDBsum; 4AUK; -.
DR PDBsum; 4B17; -.
DR AlphaFoldDB; P0ADR6; -.
DR SMR; P0ADR6; -.
DR BioGRID; 4263537; 40.
DR IntAct; P0ADR6; 14.
DR STRING; 511145.b2806; -.
DR jPOST; P0ADR6; -.
DR PaxDb; P0ADR6; -.
DR PRIDE; P0ADR6; -.
DR EnsemblBacteria; AAC75848; AAC75848; b2806.
DR EnsemblBacteria; BAE76878; BAE76878; BAE76878.
DR GeneID; 66673327; -.
DR GeneID; 947283; -.
DR KEGG; ecj:JW2777; -.
DR KEGG; eco:b2806; -.
DR PATRIC; fig|1411691.4.peg.3927; -.
DR EchoBASE; EB1742; -.
DR eggNOG; COG2933; Bacteria.
DR HOGENOM; CLU_043780_0_0_6; -.
DR InParanoid; P0ADR6; -.
DR OMA; PVDWMVC; -.
DR PhylomeDB; P0ADR6; -.
DR BioCyc; EcoCyc:EG11794-MON; -.
DR BioCyc; MetaCyc:EG11794-MON; -.
DR BRENDA; 2.1.1.186; 2026.
DR PRO; PR:P0ADR6; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0070677; F:rRNA (cytosine-2'-O-)-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0000453; P:enzyme-directed rRNA 2'-O-methylation; IMP:EcoCyc.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01551; 23SrRNA_methyltr_M; 1.
DR InterPro; IPR040739; RlmM_FDX.
DR InterPro; IPR002877; RNA_MeTrfase_FtsJ_dom.
DR InterPro; IPR011224; rRNA_MeTrfase_M.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF01728; FtsJ; 1.
DR Pfam; PF18125; RlmM_FDX; 1.
DR PIRSF; PIRSF028774; UCP028774; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Methyltransferase; Reference proteome;
KW rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..366
FT /note="Ribosomal RNA large subunit methyltransferase M"
FT /id="PRO_0000070402"
FT ACT_SITE 306
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:22923526"
FT BINDING 188
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22923526"
FT BINDING 221..224
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 240
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22923526"
FT BINDING 260
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22923526"
FT BINDING 277
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:22923526"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 13..26
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 31..34
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 40..48
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 51..58
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 61..63
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 68..73
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 86..93
FT /evidence="ECO:0007829|PDB:4AUK"
FT TURN 94..96
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 99..106
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 114..133
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 147..154
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 157..163
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 172..174
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 189..199
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 205..208
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 214..218
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 224..231
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 235..239
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 246..249
FT /evidence="ECO:0007829|PDB:4AUK"
FT TURN 250..252
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 254..257
FT /evidence="ECO:0007829|PDB:4AUK"
FT TURN 261..263
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 271..276
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 282..294
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 299..306
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 309..311
FT /evidence="ECO:0007829|PDB:4AUK"
FT HELIX 312..329
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 334..339
FT /evidence="ECO:0007829|PDB:4AUK"
FT STRAND 345..354
FT /evidence="ECO:0007829|PDB:4AUK"
SQ SEQUENCE 366 AA; 41905 MW; 595EE105DFB03677 CRC64;
MNKVVLLCRP GFEKECAAEI TDKAGQREIF GFARVKENAG YVIYECYQPD DGDKLIRELP
FSSLIFARQW FVVGELLQHL PPEDRITPIV GMLQGVVEKG GELRVEVADT NESKELLKFC
RKFTVPLRAA LRDAGVLANY ETPKRPVVHV FFIAPGCCYT GYSYSNNNSP FYMGIPRLKF
PADAPSRSTL KLEEAFHVFI PADEWDERLA NGMWAVDLGA CPGGWTYQLV KRNMWVYSVD
NGPMAQSLMD TGQVTWLRED GFKFRPTRSN ISWMVCDMVE KPAKVAALMA QWLVNGWCRE
TIFNLKLPMK KRYEEVSHNL AYIQAQLDEH GINAQIQARQ LYHDREEVTV HVRRIWAAVG
GRRDER
