Entry bact: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   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}.
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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_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         2    266       ihamap:23SrRNA_methyltr_J [T]
FT   MYHIT       241    247       ipat:N6_MTASE [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
//