RLMKL_ECOLI
ID RLMKL_ECOLI Reviewed; 702 AA.
AC P75864;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=Ribosomal RNA large subunit methyltransferase K/L;
DE Includes:
DE RecName: Full=23S rRNA m2G2445 methyltransferase;
DE EC=2.1.1.173;
DE AltName: Full=rRNA (guanine-N(2)-)-methyltransferase RlmL;
DE Includes:
DE RecName: Full=23S rRNA m7G2069 methyltransferase;
DE EC=2.1.1.264;
DE AltName: Full=rRNA (guanine-N(7)-)-methyltransferase RlmK;
GN Name=rlmL; Synonyms=rlmK, rlmKL, ycbY; OrderedLocusNames=b0948, JW0931;
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, AND CATALYTIC ACTIVITY.
RX PubMed=17010378; DOI=10.1016/j.jmb.2006.09.009;
RA Lesnyak D.V., Sergiev P.V., Bogdanov A.A., Dontsova O.A.;
RT "Identification of Escherichia coli m2G methyltransferases: I. the ycbY
RT gene encodes a methyltransferase specific for G2445 of the 23 S rRNA.";
RL J. Mol. Biol. 364:20-25(2006).
RN [5]
RP CRYSTALLIZATION.
RX PubMed=21045301; DOI=10.1107/s1744309110035074;
RA Wang K.T., Ma L., Nan J., Su X.D., Li L.;
RT "Purification, crystallization and preliminary X-ray crystallographic
RT analysis of 23S RNA m(2)G2445 methyltransferase RlmL from Escherichia
RT coli.";
RL Acta Crystallogr. F 66:1484-1486(2010).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, DOMAIN, AND MUTAGENESIS
RP OF ASP-195; ASN-309; ASN-397; ARG-530; ASP-568 AND ASP-597.
RX PubMed=22210896; DOI=10.1093/nar/gkr1287;
RA Kimura S., Ikeuchi Y., Kitahara K., Sakaguchi Y., Suzuki T., Suzuki T.;
RT "Base methylations in the double-stranded RNA by a fused methyltransferase
RT bearing unwinding activity.";
RL Nucleic Acids Res. 40:4071-4085(2012).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP SUBUNIT, AND DOMAIN.
RX PubMed=22362734; DOI=10.1093/nar/gks160;
RA Wang K.T., Desmolaize B., Nan J., Zhang X.W., Li L.F., Douthwaite S.,
RA Su X.D.;
RT "Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the
RT m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA.";
RL Nucleic Acids Res. 40:5138-5148(2012).
CC -!- FUNCTION: Specifically methylates the guanine in position 2445
CC (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA.
CC Methylation occurs before assembly of 23S rRNA into 50S subunits.
CC {ECO:0000269|PubMed:17010378, ECO:0000269|PubMed:22210896,
CC ECO:0000269|PubMed:22362734}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine(2445) in 23S rRNA + S-adenosyl-L-methionine = H(+) +
CC N(2)-methylguanosine(2445) in 23S rRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42740, Rhea:RHEA-COMP:10215, Rhea:RHEA-COMP:10216,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74269, ChEBI:CHEBI:74481; EC=2.1.1.173;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine(2069) in 23S rRNA + S-adenosyl-L-methionine = H(+) +
CC N(2)-methylguanosine(2069) in 23S rRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43772, Rhea:RHEA-COMP:10688, Rhea:RHEA-COMP:10689,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74269, ChEBI:CHEBI:74481; EC=2.1.1.264;
CC -!- ACTIVITY REGULATION: The N-terminal RlmL activity is enhanced by the C-
CC terminal RlmK activity. {ECO:0000269|PubMed:22210896}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:22362734}.
CC -!- INTERACTION:
CC P75864; P0DTT0: bipA; NbExp=3; IntAct=EBI-547718, EBI-562154;
CC P75864; P37765: rluB; NbExp=3; IntAct=EBI-547718, EBI-561550;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DOMAIN: Consists of a N-terminal RlmL domain and a C-terminal RlmK
CC domain, linked by a highly flexible loop. {ECO:0000269|PubMed:22210896,
CC ECO:0000269|PubMed:22362734}.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. RlmKL family.
CC {ECO:0000305}.
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DR EMBL; U00096; AAC74034.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35703.1; -; Genomic_DNA.
DR PIR; C64835; C64835.
DR RefSeq; NP_415468.1; NC_000913.3.
DR RefSeq; WP_001086539.1; NZ_SSZK01000002.1.
DR PDB; 3V8V; X-ray; 2.60 A; A/B=1-702.
DR PDB; 3V97; X-ray; 2.20 A; A/B=1-702.
DR PDBsum; 3V8V; -.
DR PDBsum; 3V97; -.
DR AlphaFoldDB; P75864; -.
DR SMR; P75864; -.
DR BioGRID; 4260025; 148.
DR BioGRID; 849938; 4.
DR DIP; DIP-11486N; -.
DR IntAct; P75864; 48.
DR STRING; 511145.b0948; -.
DR jPOST; P75864; -.
DR PaxDb; P75864; -.
DR PRIDE; P75864; -.
DR EnsemblBacteria; AAC74034; AAC74034; b0948.
DR EnsemblBacteria; BAA35703; BAA35703; BAA35703.
DR GeneID; 945564; -.
DR KEGG; ecj:JW0931; -.
DR KEGG; eco:b0948; -.
DR PATRIC; fig|1411691.4.peg.1326; -.
DR EchoBASE; EB3481; -.
DR eggNOG; COG0116; Bacteria.
DR eggNOG; COG1092; Bacteria.
DR HOGENOM; CLU_014042_2_0_6; -.
DR InParanoid; P75864; -.
DR OMA; WIRGYEA; -.
DR PhylomeDB; P75864; -.
DR BioCyc; EcoCyc:G6488-MON; -.
DR BioCyc; MetaCyc:G6488-MON; -.
DR BRENDA; 2.1.1.173; 2026.
DR PRO; PR:P75864; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IC:UniProtKB.
DR GO; GO:0052915; F:23S rRNA (guanine(2445)-N(2))-methyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008990; F:rRNA (guanine-N2-)-methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0070043; F:rRNA (guanine-N7-)-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0070475; P:rRNA base methylation; IMP:EcoCyc.
DR GO; GO:0031167; P:rRNA methylation; IDA:UniProtKB.
DR Gene3D; 3.40.50.150; -; 2.
DR HAMAP; MF_01858; 23SrRNA_methyltr_KL; 1.
DR InterPro; IPR017244; 23SrRNA_methyltr_KL.
DR InterPro; IPR002052; DNA_methylase_N6_adenine_CS.
DR InterPro; IPR000241; RNA_methylase_dom.
DR InterPro; IPR019614; SAM-dep_methyl-trfase.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR004114; THUMP_dom.
DR Pfam; PF10672; Methyltrans_SAM; 1.
DR Pfam; PF02926; THUMP; 1.
DR Pfam; PF01170; UPF0020; 1.
DR PIRSF; PIRSF037618; RNA_Mtase_bacteria_prd; 1.
DR SMART; SM00981; THUMP; 1.
DR SUPFAM; SSF53335; SSF53335; 2.
DR PROSITE; PS51165; THUMP; 1.
DR PROSITE; PS01261; UPF0020; 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..702
FT /note="Ribosomal RNA large subunit methyltransferase K/L"
FT /id="PRO_0000140473"
FT DOMAIN 43..154
FT /note="THUMP"
FT REGION 1..397
FT /note="RlmL"
FT REGION 398..702
FT /note="RlmK"
FT MUTAGEN 195
FT /note="D->A: Does not affect methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22210896"
FT MUTAGEN 309
FT /note="N->A: Impairs m2G2445 formation, but does not affect
FT m7G2069 formation."
FT /evidence="ECO:0000269|PubMed:22210896"
FT MUTAGEN 397
FT /note="N->A: Impairs m2G2445 formation, but does not affect
FT m7G2069 formation."
FT /evidence="ECO:0000269|PubMed:22210896"
FT MUTAGEN 530
FT /note="R->A: Does not affect methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22210896"
FT MUTAGEN 568
FT /note="D->A: Impairs m7G2069 formation, but does not affect
FT m2G2445 formation."
FT /evidence="ECO:0000269|PubMed:22210896"
FT MUTAGEN 597
FT /note="D->A: Does not affect methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22210896"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 13..22
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 26..31
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 34..39
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 41..50
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 55..65
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 69..77
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 81..84
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 91..96
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 105..121
FT /evidence="ECO:0007829|PDB:3V97"
FT TURN 122..124
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 136..144
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 147..157
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 163..165
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 175..184
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 202..211
FT /evidence="ECO:0007829|PDB:3V97"
FT TURN 216..219
FT /evidence="ECO:0007829|PDB:3V97"
FT TURN 224..227
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 233..253
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 258..263
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 265..277
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 281..283
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 284..288
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 291..293
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 305..308
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 320..336
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 341..347
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 349..353
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 359..367
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 370..378
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 393..413
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 417..423
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 430..435
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 438..443
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 454..470
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 474..476
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 477..480
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 501..505
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 508..512
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 514..519
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 524..526
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 527..536
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 541..546
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 551..558
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 562..569
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 571..583
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 591..596
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 598..604
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 609..614
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 631..645
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 646..656
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 665..670
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 673..677
FT /evidence="ECO:0007829|PDB:3V97"
FT TURN 679..682
FT /evidence="ECO:0007829|PDB:3V97"
FT HELIX 685..687
FT /evidence="ECO:0007829|PDB:3V97"
FT STRAND 695..701
FT /evidence="ECO:0007829|PDB:3V97"
SQ SEQUENCE 702 AA; 78854 MW; 9EF24AD7A32AC429 CRC64;
MNSLFASTAR GLEELLKTEL ENLGAVECQV VQGGVHFKGD TRLVYQSLMW SRLASRIMLP
LGECKVYSDL DLYLGVQAIN WTEMFNPGAT FAVHFSGLND TIRNSQYGAM KVKDAIVDAF
TRKNLPRPNV DRDAPDIRVN VWLHKETASI ALDLSGDGLH LRGYRDRAGI APIKETLAAA
IVMRSGWQPG TPLLDPMCGS GTLLIEAAML ATDRAPGLHR GRWGFSGWAQ HDEAIWQEVK
AEAQTRARKG LAEYSSHFYG SDSDARVIQR ARTNARLAGI GELITFEVKD VAQLTNPLPK
GPYGTVLSNP PYGERLDSEP ALIALHSLLG RIMKNQFGGW NLSLFSASPD LLSCLQLRAD
KQYKAKNGPL DCVQKNYHVA ESTPDSKPAM VAEDYTNRLR KNLKKFEKWA RQEGIECYRL
YDADLPEYNV AVDRYADWVV VQEYAPPKTI DAHKARQRLF DIIAATISVL GIAPNKLVLK
TRERQKGKNQ YQKLGEKGEF LEVTEYNAHL WVNLTDYLDT GLFLDHRIAR RMLGQMSKGK
DFLNLFSYTG SATVHAGLGG ARSTTTVDMS RTYLEWAERN LRLNGLTGRA HRLIQADCLA
WLREANEQFD LIFIDPPTFS NSKRMEDAFD VQRDHLALMK DLKRLLRAGG TIMFSNNKRG
FRMDLDGLAK LGLKAQEITQ KTLSQDFARN RQIHNCWLIT AA
