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Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. Unmodified tRNA is not a suitable substrate for RlmN, which suggests that RlmN works in a late step during tRNA maturation.3 Publications

Catalytic activityi

2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin.4 Publications
2 S-adenosyl-L-methionine + adenine(37) in tRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(37) in tRNA + 2 oxidized [2Fe-2S] ferredoxin.4 Publications

Cofactori

[4Fe-4S] cluster2 PublicationsNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei105 – 1051Proton acceptorSequence analysis
Metal bindingi125 – 1251Iron-sulfur (4Fe-4S-S-AdoMet)
Metal bindingi129 – 1291Iron-sulfur (4Fe-4S-S-AdoMet)
Metal bindingi132 – 1321Iron-sulfur (4Fe-4S-S-AdoMet)
Binding sitei211 – 2111S-adenosyl-L-methionine
Binding sitei312 – 3121S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen
Active sitei355 – 3551S-methylcysteine intermediate2 Publications

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • rRNA (adenine-C2-)-methyltransferase activity Source: EcoCyc
  • rRNA binding Source: UniProtKB-HAMAP
  • tRNA (adenine-C2-)-methyltransferase activity Source: UniProtKB
  • tRNA binding Source: UniProtKB

GO - Biological processi

  • response to antibiotic Source: UniProtKB-KW
  • rRNA base methylation Source: EcoCyc
  • tRNA methylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Antibiotic resistance, rRNA processing, tRNA processing

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG12401-MONOMER.
ECOL316407:JW2501-MONOMER.
MetaCyc:EG12401-MONOMER.
BRENDAi2.1.1.192. 2165.

Names & Taxonomyi

Protein namesi
Recommended name:
Dual-specificity RNA methyltransferase RlmN (EC:2.1.1.1924 Publications)
Alternative name(s):
23S rRNA (adenine(2503)-C(2))-methyltransferase
23S rRNA m2A2503 methyltransferase
Ribosomal RNA large subunit methyltransferase N
tRNA (adenine(37)-C(2))-methyltransferase
tRNA m2A37 methyltransferase
Gene namesi
Name:rlmN
Synonyms:yfgB
Ordered Locus Names:b2517, JW2501
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12401. rlmN.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene lack nucleoside m2A in both rRNA and tRNAs. Inactivation of rlmN produces an error-prone phenotype since it increases the misreading of a UAG stop codon, and thus decreases translational accuracy. Also leads to increased susceptibility to tiamulin, hygromycin A and sparsomycin.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi118 – 1181C → A: No change in iron-sulfur cluster content. No effect on methylation of Cys-355. 1 Publication
Mutagenesisi125 – 1328CALECKFC → AALEAKFA: Loss of iron-sulfur cluster binding. No methylation of Cys-355. 1 Publication
Mutagenesisi355 – 3551C → A: No change in iron-sulfur cluster content. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 384384Dual-specificity RNA methyltransferase RlmNPRO_0000171919Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi118 ↔ 355(transient)Curated

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP36979.
PRIDEiP36979.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
ftsZP0A9A63EBI-559071,EBI-370963
rplOP024133EBI-559071,EBI-543017
srmBP215073EBI-559071,EBI-546628

Protein-protein interaction databases

BioGridi4261302. 15 interactions.
DIPiDIP-12035N.
IntActiP36979. 94 interactions.
MINTiMINT-1220055.
STRINGi511145.b2517.

Structurei

Secondary structure

1
384
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi20 – 223Combined sources
Helixi25 – 3410Combined sources
Helixi39 – 5113Combined sources
Helixi57 – 593Combined sources
Helixi65 – 7410Combined sources
Beta strandi81 – 877Combined sources
Beta strandi93 – 997Combined sources
Beta strandi102 – 1109Combined sources
Beta strandi115 – 1184Combined sources
Beta strandi122 – 1243Combined sources
Helixi133 – 1353Combined sources
Beta strandi139 – 1424Combined sources
Helixi145 – 15915Combined sources
Helixi162 – 1654Combined sources
Beta strandi171 – 1755Combined sources
Beta strandi177 – 1793Combined sources
Helixi181 – 1833Combined sources
Helixi185 – 19612Combined sources
Turni198 – 2014Combined sources
Helixi205 – 2073Combined sources
Beta strandi208 – 2136Combined sources
Helixi216 – 22510Combined sources
Beta strandi229 – 2335Combined sources
Helixi239 – 2457Combined sources
Helixi247 – 2504Combined sources
Helixi254 – 26714Combined sources
Turni269 – 2735Combined sources
Beta strandi275 – 2828Combined sources
Turni283 – 2853Combined sources
Helixi289 – 29810Combined sources
Turni299 – 3013Combined sources
Beta strandi304 – 3107Combined sources
Helixi324 – 33613Combined sources
Beta strandi340 – 3434Combined sources
Beta strandi357 – 3593Combined sources
Helixi364 – 37310Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3RF9X-ray2.20A/B1-384[»]
3RFAX-ray2.05A/B1-384[»]
ProteinModelPortaliP36979.
SMRiP36979. Positions 17-375.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni179 – 1802S-adenosyl-L-methionine binding
Regioni233 – 2353S-adenosyl-L-methionine binding

Sequence similaritiesi

Belongs to the radical SAM superfamily. RlmN family.Curated

Phylogenomic databases

eggNOGiENOG4105C55. Bacteria.
COG0820. LUCA.
HOGENOMiHOG000217992.
InParanoidiP36979.
KOiK06941.
OMAiIYHFGVS.
OrthoDBiEOG6DJZ2N.
PhylomeDBiP36979.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN.
InterProiIPR013785. Aldolase_TIM.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
[Graphical view]
PANTHERiPTHR30544. PTHR30544. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF006004. CHP00048. 1 hit.
TIGRFAMsiTIGR00048. rRNA_mod_RlmN. 1 hit.

Sequencei

Sequence statusi: Complete.

P36979-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEQLVTPEN VTTKDGKINL LDLNRQQMRE FFKDLGEKPF RADQVMKWMY
60 70 80 90 100
HYCCDNFDEM TDINKVLRGK LKEVAEIRAP EVVEEQRSSD GTIKWAIAVG
110 120 130 140 150
DQRVETVYIP EDDRATLCVS SQVGCALECK FCSTAQQGFN RNLRVSEIIG
160 170 180 190 200
QVWRAAKIVG AAKVTGQRPI TNVVMMGMGE PLLNLNNVVP AMEIMLDDFG
210 220 230 240 250
FGLSKRRVTL STSGVVPALD KLGDMIDVAL AISLHAPNDE IRDEIVPINK
260 270 280 290 300
KYNIETFLAA VRRYLEKSNA NQGRVTIEYV MLDHVNDGTE HAHQLAELLK
310 320 330 340 350
DTPCKINLIP WNPFPGAPYG RSSNSRIDRF SKVLMSYGFT TIVRKTRGDD
360 370 380
IDAACGQLAG DVIDRTKRTL RKRMQGEAID IKAV
Length:384
Mass (Da):43,086
Last modified:June 1, 1994 - v1
Checksum:i92C1BDCC840FCE7B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U02965 Genomic DNA. Translation: AAA21359.1.
U00096 Genomic DNA. Translation: AAC75570.1.
AP009048 Genomic DNA. Translation: BAA16404.1.
PIRiD65028.
RefSeqiNP_417012.1. NC_000913.3.
WP_000003317.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75570; AAC75570; b2517.
BAA16404; BAA16404; BAA16404.
GeneIDi946249.
KEGGiecj:JW2501.
eco:b2517.
PATRICi32120427. VBIEscCol129921_2616.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U02965 Genomic DNA. Translation: AAA21359.1.
U00096 Genomic DNA. Translation: AAC75570.1.
AP009048 Genomic DNA. Translation: BAA16404.1.
PIRiD65028.
RefSeqiNP_417012.1. NC_000913.3.
WP_000003317.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3RF9X-ray2.20A/B1-384[»]
3RFAX-ray2.05A/B1-384[»]
ProteinModelPortaliP36979.
SMRiP36979. Positions 17-375.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261302. 15 interactions.
DIPiDIP-12035N.
IntActiP36979. 94 interactions.
MINTiMINT-1220055.
STRINGi511145.b2517.

Proteomic databases

PaxDbiP36979.
PRIDEiP36979.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75570; AAC75570; b2517.
BAA16404; BAA16404; BAA16404.
GeneIDi946249.
KEGGiecj:JW2501.
eco:b2517.
PATRICi32120427. VBIEscCol129921_2616.

Organism-specific databases

EchoBASEiEB2301.
EcoGeneiEG12401. rlmN.

Phylogenomic databases

eggNOGiENOG4105C55. Bacteria.
COG0820. LUCA.
HOGENOMiHOG000217992.
InParanoidiP36979.
KOiK06941.
OMAiIYHFGVS.
OrthoDBiEOG6DJZ2N.
PhylomeDBiP36979.

Enzyme and pathway databases

BioCyciEcoCyc:EG12401-MONOMER.
ECOL316407:JW2501-MONOMER.
MetaCyc:EG12401-MONOMER.
BRENDAi2.1.1.192. 2165.

Miscellaneous databases

PROiP36979.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN.
InterProiIPR013785. Aldolase_TIM.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
[Graphical view]
PANTHERiPTHR30544. PTHR30544. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF006004. CHP00048. 1 hit.
TIGRFAMsiTIGR00048. rRNA_mod_RlmN. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and characterization of the Escherichia coli genome between the ndk and gcpE genes."
    Baker J., Parker J.
    FEMS Microbiol. Lett. 121:293-296(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA."
    Toh S.-M., Xiong L., Bae T., Mankin A.S.
    RNA 14:98-106(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A METHYLTRANSFERASE, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE.
    Strain: K12.
  6. "Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation."
    Grove T.L., Radle M.I., Krebs C., Booker S.J.
    J. Am. Chem. Soc. 133:19586-19589(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR, MUTAGENESIS OF CYS-118; 125-CYS--CYS-132 AND CYS-355.
    Strain: K12.
  7. "A radically different mechanism for S-adenosylmethionine-dependent methyltransferases."
    Grove T.L., Benner J.S., Radle M.I., Ahlum J.H., Landgraf B.J., Krebs C., Booker S.J.
    Science 332:604-607(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A 23S RRNA A2503 METHYLTRANSFERASE, CATALYTIC ACTIVITY, REACTION MECHANISM, COVALENT METHYLCYSTEINYL INTERMEDIATE, ACTIVE SITE, REVERSIBLE DISULFIDE BOND.
    Strain: K12.
  8. "The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy."
    Benitez-Paez A., Villarroya M., Armengod M.E.
    RNA 18:1783-1795(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TRNA A37 METHYLTRANSFERASE, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE.
    Strain: K12.
  9. "Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN."
    Silakov A., Grove T.L., Radle M.I., Bauerle M.R., Green M.T., Rosenzweig A.C., Boal A.K., Booker S.J.
    J. Am. Chem. Soc. 136:8221-8228(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, REACTION MECHANISM.
  10. Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF APOENZYME AND S-METHYLCYSTEINE INTERMEDIATE IN COMPLEXES WITH IRON-SULFUR (4FE-4S) AND S-ADENOSYL-L-METHIONINE, COFACTOR, ACTIVE SITE.
    Strain: K12.

Entry informationi

Entry nameiRLMN_ECOLI
AccessioniPrimary (citable) accession number: P36979
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: May 11, 2016
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue. In details, the methyl group from one SAM molecule is initially transferred to Cys-355 in a typical SN2 displacement. Then a 5'-dA radical formed from a second molecule of SAM abstracts a hydrogen from the methyl group of mCys-355, and the resulting Cys-appended methyl radical attacks the substrate adenine ring. Methyl transfer to C2 thus results in a covalent adduct between the substrate and Cys-355, which is resolved by formation of a disulfide bond between Cys-355 and a second conserved Cys residue (Cys-118).

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.