RLMN_ECOLI
ID RLMN_ECOLI Reviewed; 384 AA.
AC P36979;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 03-AUG-2022, entry version 170.
DE RecName: Full=Dual-specificity RNA methyltransferase RlmN;
DE EC=2.1.1.192 {ECO:0000269|PubMed:18025251, ECO:0000269|PubMed:21415317, ECO:0000269|PubMed:22891362, ECO:0000269|PubMed:24806349};
DE AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase;
DE AltName: Full=23S rRNA m2A2503 methyltransferase;
DE AltName: Full=Ribosomal RNA large subunit methyltransferase N;
DE AltName: Full=tRNA (adenine(37)-C(2))-methyltransferase;
DE AltName: Full=tRNA m2A37 methyltransferase;
GN Name=rlmN; Synonyms=yfgB; OrderedLocusNames=b2517, JW2501;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=7926684; DOI=10.1111/j.1574-6968.1994.tb07115.x;
RA Baker J., Parker J.;
RT "Sequence and characterization of the Escherichia coli genome between the
RT ndk and gcpE genes.";
RL FEMS Microbiol. Lett. 121:293-296(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
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 [4]
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 [5]
RP FUNCTION AS A METHYLTRANSFERASE, CATALYTIC ACTIVITY, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12;
RX PubMed=18025251; DOI=10.1261/rna.814408;
RA Toh S.-M., Xiong L., Bae T., Mankin A.S.;
RT "The methyltransferase YfgB/RlmN is responsible for modification of
RT adenosine 2503 in 23S rRNA.";
RL RNA 14:98-106(2008).
RN [6]
RP COFACTOR, AND MUTAGENESIS OF CYS-118; 125-CYS--CYS-132 AND CYS-355.
RC STRAIN=K12;
RX PubMed=21916495; DOI=10.1021/ja207327v;
RA Grove T.L., Radle M.I., Krebs C., Booker S.J.;
RT "Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct
RT reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement
RT and radical generation.";
RL J. Am. Chem. Soc. 133:19586-19589(2011).
RN [7]
RP FUNCTION AS A 23S RRNA A2503 METHYLTRANSFERASE, CATALYTIC ACTIVITY,
RP REACTION MECHANISM, COVALENT METHYLCYSTEINYL INTERMEDIATE, ACTIVE SITE, AND
RP REVERSIBLE DISULFIDE BOND.
RC STRAIN=K12;
RX PubMed=21415317; DOI=10.1126/science.1200877;
RA Grove T.L., Benner J.S., Radle M.I., Ahlum J.H., Landgraf B.J., Krebs C.,
RA Booker S.J.;
RT "A radically different mechanism for S-adenosylmethionine-dependent
RT methyltransferases.";
RL Science 332:604-607(2011).
RN [8]
RP FUNCTION AS A TRNA A37 METHYLTRANSFERASE, CATALYTIC ACTIVITY, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=22891362; DOI=10.1261/rna.033266.112;
RA Benitez-Paez A., Villarroya M., Armengod M.E.;
RT "The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme
RT that modifies both rRNA and tRNA and controls translational accuracy.";
RL RNA 18:1783-1795(2012).
RN [9]
RP CATALYTIC ACTIVITY, AND REACTION MECHANISM.
RX PubMed=24806349; DOI=10.1021/ja410560p;
RA Silakov A., Grove T.L., Radle M.I., Bauerle M.R., Green M.T.,
RA Rosenzweig A.C., Boal A.K., Booker S.J.;
RT "Characterization of a cross-linked protein-nucleic acid substrate radical
RT in the reaction catalyzed by RlmN.";
RL J. Am. Chem. Soc. 136:8221-8228(2014).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF APOENZYME AND S-METHYLCYSTEINE
RP INTERMEDIATE IN COMPLEXES WITH IRON-SULFUR (4FE-4S) AND
RP S-ADENOSYL-L-METHIONINE, COFACTOR, AND ACTIVE SITE.
RC STRAIN=K12;
RX PubMed=21527678; DOI=10.1126/science.1205358;
RA Boal A.K., Grove T.L., McLaughlin M.I., Yennawar N.H., Booker S.J.,
RA Rosenzweig A.C.;
RT "Structural basis for methyl transfer by a radical SAM enzyme.";
RL Science 332:1089-1092(2011).
CC -!- FUNCTION: Specifically methylates position 2 of adenine 2503 in 23S
CC rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems
CC to play a crucial role in the proofreading step occurring at the
CC peptidyl transferase center and thus would serve to optimize ribosomal
CC fidelity. Unmodified tRNA is not a suitable substrate for RlmN, which
CC suggests that RlmN works in a late step during tRNA maturation.
CC {ECO:0000269|PubMed:18025251, ECO:0000269|PubMed:21415317,
CC ECO:0000269|PubMed:22891362}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin]
CC + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA +
CC 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] +
CC S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:42916, Rhea:RHEA-
CC COMP:10000, Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10152, Rhea:RHEA-
CC COMP:10282, ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192;
CC Evidence={ECO:0000269|PubMed:18025251, ECO:0000269|PubMed:21415317,
CC ECO:0000269|PubMed:22891362, ECO:0000269|PubMed:24806349};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-
CC adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-
CC deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-
CC adenosyl-L-homocysteine; Xref=Rhea:RHEA:43332, Rhea:RHEA-COMP:10000,
CC Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10162, Rhea:RHEA-COMP:10485,
CC ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192;
CC Evidence={ECO:0000269|PubMed:18025251, ECO:0000269|PubMed:21415317,
CC ECO:0000269|PubMed:22891362, ECO:0000269|PubMed:24806349};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:21527678, ECO:0000269|PubMed:21916495};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000269|PubMed:21527678, ECO:0000269|PubMed:21916495};
CC -!- INTERACTION:
CC P36979; P0A9A6: ftsZ; NbExp=3; IntAct=EBI-559071, EBI-370963;
CC P36979; P06993: malT; NbExp=3; IntAct=EBI-559071, EBI-542934;
CC P36979; P02413: rplO; NbExp=4; IntAct=EBI-559071, EBI-543017;
CC P36979; P21507: srmB; NbExp=4; IntAct=EBI-559071, EBI-546628;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene lack nucleoside m2A in
CC both rRNA and tRNAs. Inactivation of rlmN produces an error-prone
CC phenotype since it increases the misreading of a UAG stop codon, and
CC thus decreases translational accuracy. Also leads to increased
CC susceptibility to tiamulin, hygromycin A and sparsomycin.
CC {ECO:0000269|PubMed:18025251, ECO:0000269|PubMed:22891362}.
CC -!- MISCELLANEOUS: Reaction proceeds by a ping-pong mechanism involving
CC intermediate methylation of a conserved cysteine residue. In details,
CC the methyl group from one SAM molecule is initially transferred to Cys-
CC 355 in a typical SN2 displacement. Then a 5'-dA radical formed from a
CC second molecule of SAM abstracts a hydrogen from the methyl group of
CC mCys-355, and the resulting Cys-appended methyl radical attacks the
CC substrate adenine ring. Methyl transfer to C2 thus results in a
CC covalent adduct between the substrate and Cys-355, which is resolved by
CC formation of a disulfide bond between Cys-355 and a second conserved
CC Cys residue (Cys-118).
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. RlmN family.
CC {ECO:0000305}.
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DR EMBL; U02965; AAA21359.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75570.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16404.1; -; Genomic_DNA.
DR PIR; D65028; D65028.
DR RefSeq; NP_417012.1; NC_000913.3.
DR RefSeq; WP_000003317.1; NZ_STEB01000011.1.
DR PDB; 3RF9; X-ray; 2.20 A; A/B=1-384.
DR PDB; 3RFA; X-ray; 2.05 A; A/B=1-384.
DR PDB; 5HR6; X-ray; 2.88 A; A/B=1-384.
DR PDB; 5HR7; X-ray; 2.40 A; A/B=1-384.
DR PDBsum; 3RF9; -.
DR PDBsum; 3RFA; -.
DR PDBsum; 5HR6; -.
DR PDBsum; 5HR7; -.
DR AlphaFoldDB; P36979; -.
DR SMR; P36979; -.
DR BioGRID; 4261302; 67.
DR BioGRID; 850609; 4.
DR DIP; DIP-12035N; -.
DR IntAct; P36979; 95.
DR STRING; 511145.b2517; -.
DR jPOST; P36979; -.
DR PaxDb; P36979; -.
DR PRIDE; P36979; -.
DR EnsemblBacteria; AAC75570; AAC75570; b2517.
DR EnsemblBacteria; BAA16404; BAA16404; BAA16404.
DR GeneID; 66673595; -.
DR GeneID; 946249; -.
DR KEGG; ecj:JW2501; -.
DR KEGG; eco:b2517; -.
DR PATRIC; fig|1411691.4.peg.4219; -.
DR EchoBASE; EB2301; -.
DR eggNOG; COG0820; Bacteria.
DR HOGENOM; CLU_029101_0_0_6; -.
DR InParanoid; P36979; -.
DR OMA; QVGCSLD; -.
DR PhylomeDB; P36979; -.
DR BioCyc; EcoCyc:EG12401-MON; -.
DR BioCyc; MetaCyc:EG12401-MON; -.
DR BRENDA; 2.1.1.192; 2026.
DR BRENDA; 2.1.1.224; 2165.
DR BRENDA; 2.1.1.B122; 2026.
DR PRO; PR:P36979; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0070040; F:rRNA (adenine-C2-)-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0002935; F:tRNA (adenine-C2-)-methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0000049; F:tRNA binding; IDA:UniProtKB.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR GO; GO:0070475; P:rRNA base methylation; IMP:EcoCyc.
DR GO; GO:0030488; P:tRNA methylation; IDA:UniProtKB.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01849; RNA_methyltr_RlmN; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR040072; Methyltransferase_A.
DR InterPro; IPR027492; RNA_MTrfase_RlmN.
DR InterPro; IPR004383; rRNA_lsu_MTrfase_RlmN/Cfr.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR30544; PTHR30544; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF006004; CHP00048; 1.
DR SFLD; SFLDF00275; adenosine_C2_methyltransferase; 1.
DR TIGRFAMs; TIGR00048; rRNA_mod_RlmN; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Antibiotic resistance; Cytoplasm; Disulfide bond;
KW Iron; Iron-sulfur; Metal-binding; Methyltransferase; Reference proteome;
KW rRNA processing; S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..384
FT /note="Dual-specificity RNA methyltransferase RlmN"
FT /id="PRO_0000171919"
FT DOMAIN 111..350
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT ACT_SITE 105
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT ACT_SITE 355
FT /note="S-methylcysteine intermediate"
FT /evidence="ECO:0000269|PubMed:21415317,
FT ECO:0000269|PubMed:21527678"
FT BINDING 125
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 129
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 132
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 179..180
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 211
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 233..235
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 312
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT DISULFID 118..355
FT /note="(transient)"
FT /evidence="ECO:0000305"
FT MUTAGEN 118
FT /note="C->A: No change in iron-sulfur cluster content. No
FT effect on methylation of Cys-355."
FT /evidence="ECO:0000269|PubMed:21916495"
FT MUTAGEN 125..132
FT /note="CALECKFC->AALEAKFA: Loss of iron-sulfur cluster
FT binding. No methylation of Cys-355."
FT /evidence="ECO:0000269|PubMed:21916495"
FT MUTAGEN 355
FT /note="C->A: No change in iron-sulfur cluster content."
FT /evidence="ECO:0000269|PubMed:21916495"
FT HELIX 20..22
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 25..34
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 39..51
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 57..59
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 65..74
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 81..87
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 93..99
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 102..110
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 139..142
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 145..159
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 162..165
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 171..175
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 177..179
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 181..183
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 185..196
FT /evidence="ECO:0007829|PDB:3RFA"
FT TURN 198..201
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 208..213
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 216..225
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 229..233
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 239..245
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 247..250
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 254..267
FT /evidence="ECO:0007829|PDB:3RFA"
FT TURN 269..273
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 275..282
FT /evidence="ECO:0007829|PDB:3RFA"
FT TURN 283..285
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 289..298
FT /evidence="ECO:0007829|PDB:3RFA"
FT TURN 299..301
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 304..310
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 324..336
FT /evidence="ECO:0007829|PDB:3RFA"
FT STRAND 340..343
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 349..351
FT /evidence="ECO:0007829|PDB:5HR7"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:3RFA"
FT HELIX 364..373
FT /evidence="ECO:0007829|PDB:3RFA"
SQ SEQUENCE 384 AA; 43086 MW; 92C1BDCC840FCE7B CRC64;
MSEQLVTPEN VTTKDGKINL LDLNRQQMRE FFKDLGEKPF RADQVMKWMY HYCCDNFDEM
TDINKVLRGK LKEVAEIRAP EVVEEQRSSD GTIKWAIAVG DQRVETVYIP EDDRATLCVS
SQVGCALECK FCSTAQQGFN RNLRVSEIIG QVWRAAKIVG AAKVTGQRPI TNVVMMGMGE
PLLNLNNVVP AMEIMLDDFG FGLSKRRVTL STSGVVPALD KLGDMIDVAL AISLHAPNDE
IRDEIVPINK KYNIETFLAA VRRYLEKSNA NQGRVTIEYV MLDHVNDGTE HAHQLAELLK
DTPCKINLIP WNPFPGAPYG RSSNSRIDRF SKVLMSYGFT TIVRKTRGDD IDAACGQLAG
DVIDRTKRTL RKRMQGEAID IKAV
