RegulonDB RegulonDB 10.10: Gene Form
   

rsmE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gshB rsmE endA anti-terminator terminator TSS_3275 (cluster) TSS_3275 (cluster) TSS_3274 TSS_3274 TSS_3273 TSS_3273 TSS_3272 TSS_3272 TSS_3271 TSS_3271 TSS_3270 TSS_3270 rsmEp4 rsmEp4 rsmEp1 rsmEp1

Gene      
Name: rsmE    Texpresso search in the literature
Synonym(s): ECK2941, EG12366, b2946, yggJ
Genome position(nucleotides): 3091134 --> 3091865 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.14
External database links:  
ASAP:
ABE-0009665
ECHOBASE:
EB2269
ECOLIHUB:
rsmE
OU-MICROARRAY:
b2946
STRING:
511145.b2946
COLOMBOS: rsmE


Product      
Name: 16S rRNA m3U1498 methyltransferase
Synonym(s): RsmE, YggJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 26.978
Isoelectric point: 6.62
Motif(s):
 
Type Positions Sequence
20 -> 237 LCEDAANHIGRVLRMGPGQALQLFDGSNQVFDAEITSASKKSVEVKVLEGQIDDRESPLHIHLGQVMSRGEKMEFTIQKSIELGVSLITPLFSERCGVKLDSERLNKKLQQWQKIAIAACEQCGRNRVPEIRPAMDLEAWCAEQDEGLKLNLHPRASNSINTLPLPVERVRLLIGPEGGLSADEIAMTARYQFTDILLGPRVLRTETTALTAITALQV

 

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:0008168 - methyltransferase activity
GO:0016740 - transferase activity
GO:0042803 - protein homodimerization activity
GO:0070042 - rRNA (uridine-N3-)-methyltransferase activity
biological_process GO:0006364 - rRNA processing
GO:0032259 - methylation
GO:0070475 - rRNA base methylation
Note(s): Note(s): ...[more].
Reference(s): [1] Das G., et al., 2008
[2] Surkov S., et al., 2010
[3] Zhang H., et al., 2012
External database links:  
ECOCYC:
EG12366-MONOMER
ECOLIWIKI:
b2946
INTERPRO:
IPR029028
INTERPRO:
IPR029026
INTERPRO:
IPR015947
INTERPRO:
IPR006700
MODBASE:
P0AGL7
PANTHER:
PTHR30027
PDB:
4E8B
PFAM:
PF04452
PRIDE:
P0AGL7
PRODB:
PRO_000023885
REFSEQ:
NP_417421
SMR:
P0AGL7
SWISSMODEL:
P0AGL7
UNIPROT:
P0AGL7


Operon      
Name: rsmE-gshB         
Operon arrangement:
Transcription unit        Promoter
rsmE-gshB


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 rsmEp1 3091018 forward nd [ICWHO] [4]
  promoter rsmEp4 3091068 forward nd [ICWHO] [4]
  promoter TSS_3270 3091069 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3271 3091787 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3272 3091809 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3273 3092076 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3274 3092824 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3275 (cluster) 3092826 forward nd [RS-EPT-CBR] [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] Das G., Thotala DK., Kapoor S., Karunanithi S., Thakur SS., Singh NS., Varshney U., 2008, Role of 16S ribosomal RNA methylations in translation initiation in Escherichia coli., EMBO J 27(6):840-51

 [2] Surkov S., Nilsson H., Rasmussen LC., Sperling-Petersen HU., Isaksson LA., 2010, Translation initiation region dependency of translation initiation in Escherichia coli by IF1 and kasugamycin., FEBS J 277(11):2428-39

 [3] Zhang H., Wan H., Gao ZQ., Wei Y., Wang WJ., Liu GF., Shtykova EV., Xu JH., Dong YH., 2012, Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m3U1498) from crystal and solution structures., J Mol Biol 423(4):576-89

 [4] 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

 [5] 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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