RLMI_ECOLI
ID RLMI_ECOLI Reviewed; 396 AA.
AC P75876; Q9R7Q2;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 27-APR-2001, sequence version 2.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Ribosomal RNA large subunit methyltransferase I;
DE EC=2.1.1.191;
DE AltName: Full=23S rRNA m5C1962 methyltransferase;
DE AltName: Full=rRNA (cytosine-C(5)-)-methyltransferase RlmI;
GN Name=rlmI; Synonyms=yccW; OrderedLocusNames=b0967, JW5898;
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 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
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 FUNCTION AS A METHYLTRANSFERASE, AND CATALYTIC ACTIVITY.
RC STRAIN=K12;
RX PubMed=18786544; DOI=10.1016/j.jmb.2008.08.061;
RA Purta E., O'Connor M., Bujnicki J.M., Douthwaite S.;
RT "YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962.";
RL J. Mol. Biol. 383:641-651(2008).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), AND SUBUNIT.
RX PubMed=18789337; DOI=10.1016/j.jmb.2008.08.062;
RA Sunita S., Tkaczuk K.L., Purta E., Kasprzak J.M., Douthwaite S.,
RA Bujnicki J.M., Sivaraman J.;
RT "Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase
RT RlmI (YccW) reveals evolutionary links between RNA modification enzymes.";
RL J. Mol. Biol. 383:652-666(2008).
CC -!- FUNCTION: Specifically methylates the cytosine at position 1962
CC (m5C1962) of 23S rRNA. Methylation occurs before assembly of 23S rRNA
CC into 50S subunits. {ECO:0000269|PubMed:18786544}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(1962) in 23S rRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(1962) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42912, Rhea:RHEA-COMP:10382, Rhea:RHEA-COMP:10386,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.191;
CC Evidence={ECO:0000269|PubMed:18786544};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18789337}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. RlmI family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA35732.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC74053.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA35732.2; ALT_INIT; Genomic_DNA.
DR PIR; F64837; F64837.
DR RefSeq; NP_415487.4; NC_000913.3.
DR RefSeq; WP_000116297.1; NZ_SSZK01000002.1.
DR PDB; 3C0K; X-ray; 2.00 A; A/B=1-396.
DR PDBsum; 3C0K; -.
DR AlphaFoldDB; P75876; -.
DR SMR; P75876; -.
DR BioGRID; 4259463; 53.
DR DIP; DIP-11501N; -.
DR IntAct; P75876; 12.
DR STRING; 511145.b0967; -.
DR jPOST; P75876; -.
DR PaxDb; P75876; -.
DR PRIDE; P75876; -.
DR EnsemblBacteria; AAC74053; AAC74053; b0967.
DR EnsemblBacteria; BAA35732; BAA35732; BAA35732.
DR GeneID; 946691; -.
DR KEGG; ecj:JW5898; -.
DR KEGG; eco:b0967; -.
DR PATRIC; fig|511145.12.peg.1002; -.
DR EchoBASE; EB3489; -.
DR eggNOG; COG1092; Bacteria.
DR HOGENOM; CLU_014042_0_0_6; -.
DR InParanoid; P75876; -.
DR OMA; VMDVFDY; -.
DR PhylomeDB; P75876; -.
DR BioCyc; EcoCyc:G6501-MON; -.
DR BioCyc; MetaCyc:G6501-MON; -.
DR BRENDA; 2.1.1.191; 2026.
DR EvolutionaryTrace; P75876; -.
DR PRO; PR:P75876; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IC:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016434; F:rRNA (cytosine) methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0009383; F:rRNA (cytosine-C5-)-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0070475; P:rRNA base methylation; IMP:EcoCyc.
DR GO; GO:0031167; P:rRNA methylation; IDA:UniProtKB.
DR GO; GO:0044010; P:single-species biofilm formation; IMP:EcoCyc.
DR Gene3D; 2.30.130.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01857; 23SrRNA_methyltr_I; 1.
DR InterPro; IPR002478; PUA.
DR InterPro; IPR015947; PUA-like_sf.
DR InterPro; IPR036974; PUA_sf.
DR InterPro; IPR041532; RlmI_PUA-like.
DR InterPro; IPR023542; rRNA_lsu_MeTfrase_I.
DR InterPro; IPR019614; SAM-dep_methyl-trfase.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF10672; Methyltrans_SAM; 1.
DR Pfam; PF17785; PUA_3; 1.
DR SMART; SM00359; PUA; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR SUPFAM; SSF88697; SSF88697; 1.
DR PROSITE; PS50890; PUA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Methyltransferase; Reference proteome;
KW RNA-binding; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..396
FT /note="Ribosomal RNA large subunit methyltransferase I"
FT /id="PRO_0000213169"
FT DOMAIN 2..81
FT /note="PUA"
FT STRAND 4..7
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 13..16
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 20..23
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 49..55
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 59..68
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 76..97
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 107..110
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 115..120
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 131..135
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 137..147
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 151..157
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 161..164
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 170..176
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 181..187
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 190..194
FT /evidence="ECO:0007829|PDB:3C0K"
FT TURN 196..198
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 209..218
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 223..228
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 234..240
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 244..251
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 253..265
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 270..272
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 273..278
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 280..289
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 294..299
FT /evidence="ECO:0007829|PDB:3C0K"
FT TURN 304..306
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 308..312
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 317..327
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 329..339
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 346..360
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 364..371
FT /evidence="ECO:0007829|PDB:3C0K"
FT HELIX 383..385
FT /evidence="ECO:0007829|PDB:3C0K"
FT STRAND 389..395
FT /evidence="ECO:0007829|PDB:3C0K"
SQ SEQUENCE 396 AA; 44357 MW; 09C5ECEB62733D8B CRC64;
MSVRLVLAKG REKSLLRRHP WVFSGAVARM EGKASLGETI DIVDHQGKWL ARGAYSPASQ
IRARVWTFDP SESIDIAFFS RRLQQAQKWR DWLAQKDGLD SYRLIAGESD GLPGITIDRF
GNFLVLQLLS AGAEYQRAAL ISALQTLYPE CSIYDRSDVA VRKKEGMELT QGPVTGELPP
ALLPIEEHGM KLLVDIQHGH KTGYYLDQRD SRLATRRYVE NKRVLNCFSY TGGFAVSALM
GGCSQVVSVD TSQEALDIAR QNVELNKLDL SKAEFVRDDV FKLLRTYRDR GEKFDVIVMD
PPKFVENKSQ LMGACRGYKD INMLAIQLLN EGGILLTFSC SGLMTSDLFQ KIIADAAIDA
GRDVQFIEQF RQAADHPVIA TYPEGLYLKG FACRVM
