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 10-MAY-2017, entry version 123.
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
RT region 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.,
RA Mau B., 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
RT MG1655 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
RT competitive 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
RT 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.,
RA Serebryakova M.V., Bogdanov A.A., Dontsova O.A.;
RT "The last rRNA methyltransferase of E. coli revealed: the yhiR gene
RT encodes adenine-N6 methyltransferase specific for modification of
RT A2030 of 23S 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
RT analysis of the 23S rRNA methyltransferase RlmJ from Escherichia
RT coli.";
RL Acta Crystallogr. F 69:1001-1003(2013).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF APOENZYME AND IN COMPLEXES
RP WITH S-ADENOSYL-L-HOMOCYSTEINE AND SUBSTRATE ANALOG, FUNCTION,
RP CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ACTIVE SITE, AND
RP MUTAGENESIS OF TYR-4; 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
RT rRNA m6A methyltransferase RlmJ.";
RL Nucleic Acids Res. 41:9537-9548(2013).
CC -!- FUNCTION: Specifically methylates the adenine in position 2030 of
CC 23S rRNA. Nascent 23S rRNA seems to be the natural substrate.
CC Appears to be not necessary for ribosome assembly. Required for
CC the utilization of extracellular DNA as the sole source of carbon
CC and energy (PubMed:11591672, PubMed:16707682). {ECO:0000255|HAMAP-
CC Rule:MF_00934, ECO:0000269|PubMed:11591672,
CC ECO:0000269|PubMed:16707682, ECO:0000269|PubMed:22847818,
CC ECO:0000269|PubMed:23945937}.
CC -!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + adenine(2030) in 23S
CC rRNA = S-adenosyl-L-homocysteine + N(6)-methyladenine(2030) in 23S
CC rRNA. {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 -!- DISRUPTION PHENOTYPE: The inactivation of the this gene results in
CC the complete loss of A2030 modification, but does not cause the
CC accumulation of ribosome assembly intermediates. The phenotype of
CC rlmJ knockout gene is very mild under various growth conditions
CC and at the stationary phase, except for a small growth advantage
CC in anaerobic conditions. Only minor changes in the total E.coli
CC proteome can be observed in a cell devoid of the 23S rRNA
CC nucleotide A2030 methylation (PubMed:22847818). Mutants show a
CC stationary-phase competition defect during coculture with wild-
CC type cells (PubMed:11591672). Cells lacking this gene are unable
CC to grow using DNA as a sole nutrition source, but have no defects
CC in DNA uptake by electroporation or when made chemically competent
CC (PubMed:11591672, PubMed:16707682). {ECO:0000269|PubMed:11591672,
CC ECO:0000269|PubMed:16707682, ECO:0000269|PubMed:22847818}.
CC -!- MISCELLANEOUS: Recombinant protein prefers protein-free 23S rRNA
CC to ribonucleoprotein particles containing only part of the 50S
CC subunit 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
CC the 23S RNA is completely transcribed, processed and folded
CC (PubMed:23945937). Cannot modify single-stranded DNA having the
CC same sequence as H72 (PubMed:23945937).
CC {ECO:0000305|PubMed:22847818, ECO:0000305|PubMed:23945937}.
CC -!- SIMILARITY: Belongs to the RlmJ family. {ECO:0000255|HAMAP-
CC Rule:MF_00934}.
CC -----------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution-NoDerivs License
CC -----------------------------------------------------------------------
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_LN832404.1.
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 PDBsum; 4BLU; -.
DR PDBsum; 4BLV; -.
DR PDBsum; 4BLW; -.
DR ProteinModelPortal; P37634; -.
DR SMR; P37634; -.
DR BioGrid; 4262505; 7.
DR DIP; DIP-12371N; -.
DR IntAct; P37634; 20.
DR MINT; MINT-1219143; -.
DR STRING; 511145.b3499; -.
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; 32122448; VBIEscCol129921_3601.
DR EchoBASE; EB2146; -.
DR EcoGene; EG12234; rlmJ.
DR eggNOG; ENOG4105D6S; Bacteria.
DR eggNOG; COG2961; LUCA.
DR HOGENOM; HOG000262479; -.
DR InParanoid; P37634; -.
DR KO; K07115; -.
DR OMA; TYAIWYP; -.
DR PhylomeDB; P37634; -.
DR BioCyc; EcoCyc:EG12234-MONOMER; -.
DR BioCyc; MetaCyc:EG12234-MONOMER; -.
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-KW.
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 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.
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; Complete proteome; Methyltransferase;
KW Reference proteome; RNA-binding; rRNA processing;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1 280 Ribosomal RNA large subunit
FT methyltransferase J.
FT /FTId=PRO_0000169567.
FT REGION 143 144 S-adenosyl-L-methionine binding.
FT {ECO:0000305|PubMed:23945937}.
FT ACT_SITE 164 164 Proton acceptor.
FT {ECO:0000305|PubMed:23945937}.
FT BINDING 19 19 S-adenosyl-L-methionine.
FT {ECO:0000305|PubMed:23945937}.
FT BINDING 42 42 S-adenosyl-L-methionine; via carbonyl
FT oxygen. {ECO:0000305|PubMed:23945937}.
FT BINDING 100 100 S-adenosyl-L-methionine.
FT {ECO:0000305|PubMed:23945937}.
FT BINDING 118 118 S-adenosyl-L-methionine.
FT {ECO:0000305|PubMed:23945937}.
FT BINDING 164 164 S-adenosyl-L-methionine.
FT {ECO:0000305|PubMed:23945937}.
FT SITE 4 4 Interaction with substrate rRNA.
FT {ECO:0000305}.
FT MUTAGEN 4 4 Y->A: Loss of catalytic activity.
FT {ECO:0000269|PubMed:23945937}.
FT MUTAGEN 4 4 Y->F: 40-fold reduction in catalytic
FT activity. {ECO:0000269|PubMed:23945937}.
FT MUTAGEN 6 6 H->D: Loss of catalytic activity.
FT {ECO:0000269|PubMed:23945937}.
FT MUTAGEN 18 18 K->A: Loss of catalytic activity.
FT {ECO:0000269|PubMed:23945937}.
FT MUTAGEN 18 18 K->R: 10-fold reduction in catalytic
FT activity. {ECO:0000269|PubMed:23945937}.
FT MUTAGEN 164 164 D->A: Loss of catalytic activity.
FT {ECO:0000269|PubMed:23945937}.
FT HELIX 6 8 {ECO:0000244|PDB:4BLW}.
FT TURN 9 11 {ECO:0000244|PDB:4BLW}.
FT HELIX 13 29 {ECO:0000244|PDB:4BLU}.
FT STRAND 32 34 {ECO:0000244|PDB:4BLU}.
FT STRAND 37 42 {ECO:0000244|PDB:4BLU}.
FT STRAND 45 49 {ECO:0000244|PDB:4BLU}.
FT STRAND 53 56 {ECO:0000244|PDB:4BLU}.
FT HELIX 60 63 {ECO:0000244|PDB:4BLU}.
FT HELIX 65 67 {ECO:0000244|PDB:4BLU}.
FT TURN 68 70 {ECO:0000244|PDB:4BLU}.
FT HELIX 76 78 {ECO:0000244|PDB:4BLU}.
FT HELIX 79 87 {ECO:0000244|PDB:4BLU}.
FT TURN 88 91 {ECO:0000244|PDB:4BLV}.
FT STRAND 96 98 {ECO:0000244|PDB:4BLU}.
FT HELIX 100 107 {ECO:0000244|PDB:4BLU}.
FT STRAND 113 117 {ECO:0000244|PDB:4BLU}.
FT HELIX 123 130 {ECO:0000244|PDB:4BLU}.
FT TURN 131 133 {ECO:0000244|PDB:4BLU}.
FT STRAND 137 140 {ECO:0000244|PDB:4BLU}.
FT TURN 144 146 {ECO:0000244|PDB:4BLU}.
FT HELIX 147 150 {ECO:0000244|PDB:4BLU}.
FT STRAND 159 163 {ECO:0000244|PDB:4BLU}.
FT HELIX 170 186 {ECO:0000244|PDB:4BLU}.
FT STRAND 190 200 {ECO:0000244|PDB:4BLU}.
FT HELIX 201 213 {ECO:0000244|PDB:4BLU}.
FT STRAND 219 227 {ECO:0000244|PDB:4BLU}.
FT STRAND 231 234 {ECO:0000244|PDB:4BLU}.
FT STRAND 237 244 {ECO:0000244|PDB:4BLU}.
FT HELIX 249 264 {ECO:0000244|PDB:4BLU}.
FT STRAND 270 278 {ECO:0000244|PDB:4BLU}.
CC --------------------------------------------------------------------------
CC The following FT lines are automated annotations from the MyHits database.
CC --------------------------------------------------------------------------
FT MYHIT 241 247 ipat:N6_MTASE [T]
FT MYHIT 2 266 ihamap:23SrRNA_methyltr_J [T]
FT MYHIT 33 278 ipfam:RsmJ [T]
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
//
|
