RegulonDB RegulonDB 11.1: Gene Form
   

rlmN gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rlmN rodZ ndk terminator TSS_2817 TSS_2817 rodZp2 rodZp2 rodZp1 rodZp1 TSS_2816 TSS_2816 TSS_2815 TSS_2815 TSS_2814 (cluster) TSS_2814 (cluster) TSS_2813 (cluster) TSS_2813 (cluster) ispGp5 ispGp5 ispGp4 ispGp4 TSS_2812 TSS_2812 TSS_2811 (cluster) TSS_2811 (cluster) TSS_2810 TSS_2810 ispGp1 ispGp1

Gene      
Name: rlmN    Texpresso search in the literature
Synonym(s): ECK2513, EG12401, b2517, yfgB
Genome position(nucleotides): 2643129 <-- 2644283
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.99
External database links:  
ASAP:
 ABE-0008287
ECHOBASE:
 EB2301
ECOLIHUB:
 rlmN
OU-MICROARRAY:
 b2517
STRING:
 511145.b2517
COLOMBOS: rlmN


Product      
Name: 23S rRNA m2A2503 methyltransferase/tRNA m2A37 methyltransferase
Synonym(s): RlmN, YfgB, ribosomal RNA large subunit methyltransferase N
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 43.086
Isoelectric point: 6.985
Motif(s):
 
Type Positions Sequence Comment
111 -> 350 EDDRATLCVSSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDD UniProt: Radical SAM core.
118 -> 118 C UniProt: No change in iron-sulfur cluster content. No effect on methylation of Cys-355..
120 -> 289 SSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGT
125 -> 132 CALECKFC UniProt: Loss of iron-sulfur cluster binding. No methylation of Cys-355..
179 -> 180 GE UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0008168 - methyltransferase activity
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0008173 - RNA methyltransferase activity
GO:0000049 - tRNA binding
GO:0019843 - rRNA binding
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0070040 - rRNA (adenine-C2-)-methyltransferase activity
GO:0002935 - tRNA (adenine-C2-)-methyltransferase activity
biological_process GO:0030488 - tRNA methylation
GO:0046677 - response to antibiotic
GO:0008033 - tRNA processing
GO:0006364 - rRNA processing
GO:0032259 - methylation
GO:0070475 - rRNA base methylation
Note(s): Note(s): ...[more].
Reference(s): [1] Atkinson GC., et al., 2013
[2] Hussain S. 2019
[3] Lanz ND., et al., 2012
[4] Stojkovic V., et al., 2015
[5] Stojkovic V., et al., 2021
[6] Zhao C., et al., 2017
External database links:  
ALPHAFOLD:
 P36979
DIP:
 DIP-12035N
ECOCYC:
 EG12401-MONOMER
ECOLIWIKI:
 b2517
INTERPRO:
 IPR013785
INTERPRO:
 IPR007197
INTERPRO:
 IPR004383
INTERPRO:
 IPR040072
INTERPRO:
 IPR027492
MODBASE:
 P36979
PANTHER:
 PTHR30544
PDB:
 3RF9
PDB:
 3RFA
PDB:
 5HR7
PDB:
 5HR6
PFAM:
 PF04055
PRIDE:
 P36979
PRODB:
 PRO_000023774
PROSITE:
 PS51918
REFSEQ:
 NP_417012
SMR:
 P36979
UNIPROT:
 P36979


Operon      
Name: rlmN         
Operon arrangement:
Transcription unit        Promoter
rlmN


RNA cis-regulatory element    
Attenuation: Translational


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter ispGp1 2641880 reverse nd [COMP-AINF] [7]
  promoter TSS_2810 2641922 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2811 (cluster) 2641929 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2812 2641933 reverse nd [RS-EPT-CBR] [8]
  promoter ispGp4 2641950 reverse nd [COMP-AINF] [7]
  promoter ispGp5 2641954 reverse nd [COMP-AINF] [7]
  promoter TSS_2813 (cluster) 2641985 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2814 (cluster) 2641990 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2815 2641997 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2816 2642045 reverse nd [RS-EPT-CBR] [8]
  promoter rodZp1 2642932 reverse nd [COMP-AINF] [7]
  promoter rodZp2 2642934 reverse nd [COMP-AINF] [7]
  promoter TSS_2817 2644379 reverse nd [RS-EPT-CBR] [8]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Atkinson GC., Hansen LH., Tenson T., Rasmussen A., Kirpekar F., Vester B., 2013, Distinction between the Cfr methyltransferase conferring antibiotic resistance and the housekeeping RlmN methyltransferase., Antimicrob Agents Chemother 57(8):4019-26

 [2] Hussain S., 2019, Catalytic crosslinking-based methods for enzyme-specified profiling of RNA ribonucleotide modifications., Methods 156:60-65

 [3] Lanz ND., Grove TL., Gogonea CB., Lee KH., Krebs C., Booker SJ., 2012, RlmN and AtsB as models for the overproduction and characterization of radical SAM proteins., Methods Enzymol 516:125-52

 [4] Stojkovic V., Fujimori DG., 2015, Radical SAM-Mediated Methylation of Ribosomal RNA., Methods Enzymol 560:355-76

 [5] Stojkovic V., Weinberg DE., Fujimori DG., 2021, miCLIP-MaPseq Identifies Substrates of Radical SAM RNA-Methylating Enzyme Using Mechanistic Cross-Linking and Mismatch Profiling., Methods Mol Biol 2298:105-122

 [6] Zhao C., Dong L., Liu Y., 2017, A QM/MM study of the catalytic mechanism of SAM methyltransferase RlmN from Escherichia coli., Proteins 85(11):1967-1974

 [7] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [8] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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