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Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

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).

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)DescriptionActionsGraphical viewLength
Active sitei105Proton acceptorSequence analysis1
Metal bindingi125Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi129Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi132Iron-sulfur (4Fe-4S-S-AdoMet)1
Binding sitei211S-adenosyl-L-methionine1
Binding sitei312S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen1
Active sitei355S-methylcysteine intermediate2 Publications1

GO - Molecular functioni

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

Keywordsi

Molecular functionMethyltransferase, Transferase
Biological processAntibiotic resistance, rRNA processing, tRNA processing
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG12401-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12401 rlmN

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

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)DescriptionActionsGraphical viewLength
Mutagenesisi118C → A: No change in iron-sulfur cluster content. No effect on methylation of Cys-355. 1 Publication1
Mutagenesisi125 – 132CALECKFC → AALEAKFA: Loss of iron-sulfur cluster binding. No methylation of Cys-355. 1 Publication8
Mutagenesisi355C → A: No change in iron-sulfur cluster content. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001719191 – 384Dual-specificity RNA methyltransferase RlmNAdd BLAST384

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi118 ↔ 355(transient)Curated

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP36979
PRIDEiP36979

Interactioni

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4261302, 67 interactors
DIPiDIP-12035N
IntActiP36979, 95 interactors
STRINGi316385.ECDH10B_2683

Structurei

Secondary structure

1384
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi20 – 22Combined sources3
Helixi25 – 34Combined sources10
Helixi39 – 51Combined sources13
Helixi57 – 59Combined sources3
Helixi65 – 74Combined sources10
Beta strandi81 – 87Combined sources7
Beta strandi93 – 99Combined sources7
Beta strandi102 – 110Combined sources9
Beta strandi115 – 118Combined sources4
Beta strandi122 – 124Combined sources3
Helixi133 – 135Combined sources3
Beta strandi139 – 142Combined sources4
Helixi145 – 159Combined sources15
Helixi162 – 165Combined sources4
Beta strandi171 – 175Combined sources5
Beta strandi177 – 179Combined sources3
Helixi181 – 183Combined sources3
Helixi185 – 196Combined sources12
Turni198 – 201Combined sources4
Helixi205 – 207Combined sources3
Beta strandi208 – 213Combined sources6
Helixi216 – 225Combined sources10
Beta strandi229 – 233Combined sources5
Helixi239 – 245Combined sources7
Helixi247 – 250Combined sources4
Helixi254 – 267Combined sources14
Turni269 – 273Combined sources5
Beta strandi275 – 282Combined sources8
Turni283 – 285Combined sources3
Helixi289 – 298Combined sources10
Turni299 – 301Combined sources3
Beta strandi304 – 310Combined sources7
Helixi324 – 336Combined sources13
Beta strandi340 – 343Combined sources4
Helixi349 – 351Combined sources3
Beta strandi357 – 359Combined sources3
Helixi364 – 373Combined sources10

3D structure databases

ProteinModelPortaliP36979
SMRiP36979
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni179 – 180S-adenosyl-L-methionine binding2
Regioni233 – 235S-adenosyl-L-methionine binding3

Sequence similaritiesi

Belongs to the radical SAM superfamily. RlmN family.Curated

Phylogenomic databases

eggNOGiENOG4105C55 Bacteria
COG0820 LUCA
HOGENOMiHOG000217992
InParanoidiP36979
KOiK06941
OMAiCGQLANK
PhylomeDBiP36979

Family and domain databases

Gene3Di3.20.20.70, 1 hit
HAMAPiMF_01849 RNA_methyltr_RlmN, 1 hit
InterProiView protein in InterPro
IPR013785 Aldolase_TIM
IPR027492 RNA_MTrfase_RlmN
IPR004383 rRNA_lsu_MTrfase_RlmN/Cfr
IPR007197 rSAM
PANTHERiPTHR30544 PTHR30544, 1 hit
PfamiView protein in Pfam
PF04055 Radical_SAM, 1 hit
PIRSFiPIRSF006004 CHP00048, 1 hit
SFLDiSFLDF00275 adenosine_C2_methyltransferase, 1 hit
SFLDS00029 Radical_SAM, 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
PATRICifig|1411691.4.peg.4219

Similar proteinsi

Entry informationi

Entry nameiRLMN_ECOLI
AccessioniPrimary (citable) accession number: P36979
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: March 28, 2018
This is version 147 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

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