RLMJ_ECOLI
ID RLMJ_ECOLI Reviewed; 280 AA.
AC P37634; Q2M7G1;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Ribosomal RNA large subunit methyltransferase J {ECO:0000255|HAMAP-Rule:MF_00934};
DE EC=2.1.1.266 {ECO:0000255|HAMAP-Rule:MF_00934};
DE AltName: Full=23S rRNA (adenine(2030)-N6)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_00934};
DE AltName: Full=23S rRNA m6A2030 methyltransferase {ECO:0000255|HAMAP-Rule:MF_00934};
GN Name=rlmJ {ECO:0000255|HAMAP-Rule:MF_00934}; Synonyms=yhiR;
GN OrderedLocusNames=b3499, JW3466;
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=8041620; DOI=10.1093/nar/22.13.2576;
RA Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.;
RT "Analysis of the Escherichia coli genome. V. DNA sequence of the region
RT from 76.0 to 81.5 minutes.";
RL Nucleic Acids Res. 22:2576-2586(1994).
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 DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ZK126;
RX PubMed=16707682; DOI=10.1128/jb.01974-05;
RA Palchevskiy V., Finkel S.E.;
RT "Escherichia coli competence gene homologs are essential for competitive
RT fitness and the use of DNA as a nutrient.";
RL J. Bacteriol. 188:3902-3910(2006).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ZK126;
RX PubMed=11591672; DOI=10.1128/jb.183.21.6288-6293.2001;
RA Finkel S.E., Kolter R.;
RT "DNA as a nutrient: novel role for bacterial competence gene homologs.";
RL J. Bacteriol. 183:6288-6293(2001).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, GENE NAME, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=22847818; DOI=10.1261/rna.034207.112;
RA Golovina A.Y., Dzama M.M., Osterman I.A., Sergiev P.V., Serebryakova M.V.,
RA Bogdanov A.A., Dontsova O.A.;
RT "The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes
RT adenine-N6 methyltransferase specific for modification of A2030 of 23S
RT ribosomal RNA.";
RL RNA 18:1725-1734(2012).
RN [7]
RP CRYSTALLIZATION, AND SUBUNIT.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=23989148; DOI=10.1107/s1744309113020289;
RA Punekar A.S., Selmer M.;
RT "Purification, crystallization and preliminary X-ray diffraction analysis
RT of the 23S rRNA methyltransferase RlmJ from Escherichia coli.";
RL Acta Crystallogr. F 69:1001-1003(2013).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP S-ADENOSYL-L-HOMOCYSTEINE AND SUBSTRATE ANALOG, FUNCTION, CATALYTIC
RP ACTIVITY, SUBSTRATE SPECIFICITY, ACTIVE SITE, AND MUTAGENESIS OF TYR-4;
RP HIS-6; LYS-18 AND ASP-164.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=23945937; DOI=10.1093/nar/gkt719;
RA Punekar A.S., Liljeruhm J., Shepherd T.R., Forster A.C., Selmer M.;
RT "Structural and functional insights into the molecular mechanism of rRNA
RT m6A methyltransferase RlmJ.";
RL Nucleic Acids Res. 41:9537-9548(2013).
CC -!- FUNCTION: Specifically methylates the adenine in position 2030 of 23S
CC rRNA. Nascent 23S rRNA seems to be the natural substrate. Appears to be
CC not necessary for ribosome assembly. Required for the utilization of
CC extracellular DNA as the sole source of carbon and energy
CC (PubMed:11591672, PubMed:16707682). {ECO:0000255|HAMAP-Rule:MF_00934,
CC ECO:0000269|PubMed:11591672, ECO:0000269|PubMed:16707682,
CC ECO:0000269|PubMed:22847818, ECO:0000269|PubMed:23945937}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(2030) in 23S rRNA + S-adenosyl-L-methionine = H(+) +
CC N(6)-methyladenosine(2030) in 23S rRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43736, Rhea:RHEA-COMP:10668, Rhea:RHEA-COMP:10669,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74449; EC=2.1.1.266;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00934,
CC ECO:0000269|PubMed:22847818, ECO:0000269|PubMed:23945937};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00934,
CC ECO:0000269|PubMed:23989148}.
CC -!- INTERACTION:
CC P37634; P0A8H6: yihI; NbExp=2; IntAct=EBI-548165, EBI-552497;
CC -!- DISRUPTION PHENOTYPE: The inactivation of the this gene results in the
CC complete loss of A2030 modification, but does not cause the
CC accumulation of ribosome assembly intermediates. The phenotype of rlmJ
CC knockout gene is very mild under various growth conditions and at the
CC stationary phase, except for a small growth advantage in anaerobic
CC conditions. Only minor changes in the total E.coli proteome can be
CC observed in a cell devoid of the 23S rRNA nucleotide A2030 methylation
CC (PubMed:22847818). Mutants show a stationary-phase competition defect
CC during coculture with wild-type cells (PubMed:11591672). Cells lacking
CC this gene are unable to grow using DNA as a sole nutrition source, but
CC have no defects in DNA uptake by electroporation or when made
CC chemically competent (PubMed:11591672, PubMed:16707682).
CC {ECO:0000269|PubMed:11591672, ECO:0000269|PubMed:16707682,
CC ECO:0000269|PubMed:22847818}.
CC -!- MISCELLANEOUS: Recombinant protein prefers protein-free 23S rRNA to
CC ribonucleoprotein particles containing only part of the 50S subunit
CC proteins and does not methylate the assembled 50S subunit
CC (PubMed:22847818). Recognizes a minimal substrate corresponding to
CC helix 72; this shows that RlmJ requires only a small hairpin for
CC activity and this suggests that RlmJ can methylate A2030 before the 23S
CC RNA is completely transcribed, processed and folded (PubMed:23945937).
CC Cannot modify single-stranded DNA having the same sequence as H72
CC (PubMed:23945937). {ECO:0000305|PubMed:22847818,
CC ECO:0000305|PubMed:23945937}.
CC -!- SIMILARITY: Belongs to the RlmJ family. {ECO:0000255|HAMAP-
CC Rule:MF_00934}.
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DR EMBL; U00039; AAB18475.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76524.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77795.1; -; Genomic_DNA.
DR PIR; S47719; S47719.
DR RefSeq; NP_417956.1; NC_000913.3.
DR RefSeq; WP_001300574.1; NZ_SSZK01000042.1.
DR PDB; 4BLU; X-ray; 1.85 A; A/B=1-280.
DR PDB; 4BLV; X-ray; 2.00 A; A/B=1-280.
DR PDB; 4BLW; X-ray; 1.95 A; A/B=1-280.
DR PDB; 6QDX; X-ray; 2.10 A; A/B/C/D=1-280.
DR PDB; 6QE0; X-ray; 1.39 A; A=1-280.
DR PDB; 6QE5; X-ray; 1.61 A; A/B=1-280.
DR PDBsum; 4BLU; -.
DR PDBsum; 4BLV; -.
DR PDBsum; 4BLW; -.
DR PDBsum; 6QDX; -.
DR PDBsum; 6QE0; -.
DR PDBsum; 6QE5; -.
DR AlphaFoldDB; P37634; -.
DR SMR; P37634; -.
DR BioGRID; 4262505; 18.
DR DIP; DIP-12371N; -.
DR IntAct; P37634; 20.
DR STRING; 511145.b3499; -.
DR jPOST; P37634; -.
DR PaxDb; P37634; -.
DR PRIDE; P37634; -.
DR EnsemblBacteria; AAC76524; AAC76524; b3499.
DR EnsemblBacteria; BAE77795; BAE77795; BAE77795.
DR GeneID; 948012; -.
DR KEGG; ecj:JW3466; -.
DR KEGG; eco:b3499; -.
DR PATRIC; fig|511145.12.peg.3601; -.
DR EchoBASE; EB2146; -.
DR eggNOG; COG2961; Bacteria.
DR HOGENOM; CLU_061769_0_0_6; -.
DR InParanoid; P37634; -.
DR OMA; TYAIWYP; -.
DR PhylomeDB; P37634; -.
DR BioCyc; EcoCyc:EG12234-MON; -.
DR BioCyc; MetaCyc:EG12234-MON; -.
DR BRENDA; 2.1.1.266; 2026.
DR PRO; PR:P37634; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0036307; F:23S rRNA (adenine(2030)-N(6))-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008988; F:rRNA (adenine-N6-)-methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0015976; P:carbon utilization; IMP:EcoCyc.
DR GO; GO:0070475; P:rRNA base methylation; IDA:UniProtKB.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_00934; 23SrRNA_methyltr_J; 1.
DR InterPro; IPR002052; DNA_methylase_N6_adenine_CS.
DR InterPro; IPR007473; RlmJ.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR37426; PTHR37426; 1.
DR Pfam; PF04378; RsmJ; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS00092; N6_MTASE; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Methyltransferase; Reference proteome; RNA-binding;
KW rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..280
FT /note="Ribosomal RNA large subunit methyltransferase J"
FT /id="PRO_0000169567"
FT ACT_SITE 164
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:23945937"
FT BINDING 19
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:23945937"
FT BINDING 42
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:23945937"
FT BINDING 100
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:23945937"
FT BINDING 118
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:23945937"
FT BINDING 143..144
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:23945937"
FT BINDING 164
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:23945937"
FT SITE 4
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000305"
FT MUTAGEN 4
FT /note="Y->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23945937"
FT MUTAGEN 4
FT /note="Y->F: 40-fold reduction in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23945937"
FT MUTAGEN 6
FT /note="H->D: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23945937"
FT MUTAGEN 18
FT /note="K->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23945937"
FT MUTAGEN 18
FT /note="K->R: 10-fold reduction in catalytic activity."
FT /evidence="ECO:0000269|PubMed:23945937"
FT MUTAGEN 164
FT /note="D->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23945937"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:6QE5"
FT TURN 9..11
FT /evidence="ECO:0007829|PDB:6QE5"
FT HELIX 13..29
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 37..42
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 45..49
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 53..56
FT /evidence="ECO:0007829|PDB:4BLU"
FT HELIX 60..62
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:6QE0"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 76..78
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 79..87
FT /evidence="ECO:0007829|PDB:6QE0"
FT TURN 88..91
FT /evidence="ECO:0007829|PDB:4BLV"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 100..107
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 113..117
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 123..130
FT /evidence="ECO:0007829|PDB:6QE0"
FT TURN 131..133
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 144..150
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 159..163
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 172..186
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 190..200
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 201..213
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 219..227
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 231..234
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 237..244
FT /evidence="ECO:0007829|PDB:6QE0"
FT HELIX 249..264
FT /evidence="ECO:0007829|PDB:6QE0"
FT STRAND 270..278
FT /evidence="ECO:0007829|PDB:6QE0"
SQ SEQUENCE 280 AA; 31942 MW; 13B039C77C5B77A7 CRC64;
MLSYRHSFHA GNHADVLKHT VQSLIIESLK EKDKPFLYLD THAGAGRYQL GSEHAERTGE
YLEGIARIWQ QDDLPAELEA YINVVKHFNR SGQLRYYPGS PLIARLLLRE QDSLQLTELH
PSDYPLLRSE FQKDSRARVE KADGFQQLKA KLPPVSRRGL ILIDPPYEMK TDYQAVVSGI
AEGYKRFATG IYALWYPVVL RQQIKRMIHD LEATGIRKIL QIELAVLPDS DRRGMTASGM
IVINPPWKLE QQMNNVLPWL HSKLVPAGTG HATVSWIVPE
