RegulonDB RegulonDB 10.9: Gene Form
   

rlmE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ftsH rlmE yhbY anti-anti-terminator TSS_3488 TSS_3488 rlmEp1 rlmEp1 yhbYp yhbYp rlmEp2 rlmEp2 TSS_3487 TSS_3487 TSS_3486 (cluster) TSS_3486 (cluster) ftsHp1 ftsHp1 ftsHp4 ftsHp4 TSS_3484 TSS_3484 TSS_3483 TSS_3483 TSS_3482 TSS_3482 TSS_3481 TSS_3481 TSS_3480 TSS_3480

Gene      
Name: rlmE    Texpresso search in the literature
Synonym(s): ECK3168, EG11507, b3179, ftsJ, mrsF, rrmJ
Genome position(nucleotides): 3327035 <-- 3327664 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.48
External database links:  
ASAP:
ABE-0010447
CGSC:
33511
ECHOBASE:
EB1470
ECOLIHUB:
rlmE
OU-MICROARRAY:
b3179
STRING:
511145.b3179
COLOMBOS: rlmE


Product      
Name: 23S rRNA 2'-O-ribose U2552 methyltransferase
Synonym(s): FtsJ, MrsF, RlmE, RrmJ, ribosomal RNA large subunit methyltransferase E
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 23.335
Isoelectric point: 9.955
Motif(s):
 
Type Positions Sequence
38 -> 38 K
83 -> 83 D
31 -> 206 LRSRAWFKLDEIQQSDKLFKPGMTVVDLGAAPGGWSQYVVTQIGGKGRIIACDLLPMDPIVGVDFLQGDFRDELVMKALLERVGDSKVQVVMSDMAPNMSGTPAVDIPRAMYLVELALEMCRDVLAPGGSFVVKVFQGEGFDEYLREIRSLFTKVKVRKPDSSRARSREVYIVATG
34 -> 34 R
199 -> 199 E

 

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:0008173 - RNA methyltransferase activity
GO:0016436 - rRNA (uridine) methyltransferase activity
GO:0008650 - rRNA (uridine-2'-O-)-methyltransferase activity
biological_process GO:0001510 - RNA methylation
GO:0000027 - ribosomal large subunit assembly
GO:0006364 - rRNA processing
GO:0032259 - methylation
GO:0000453 - enzyme-directed rRNA 2'-O-methylation
Note(s): Note(s): ...[more].
Reference(s): [1] Feder M., et al., 2003
[2] Ishiguro K., et al., 2019
[3] Porta JM., et al., 2013
[4] Sergiev PV., et al., 2012
[5] Siibak T., et al., 2010
External database links:  
DIP:
DIP-47902N
ECOCYC:
EG11507-MONOMER
ECOLIWIKI:
b3179
ECOO157CYC:
FTSJ-MONOMER
INTERPRO:
IPR002877
INTERPRO:
IPR029063
INTERPRO:
IPR015507
INTERPRO:
IPR004512
MODBASE:
P0C0R7
PDB:
1EJ0
PDB:
1EIZ
PFAM:
PF01728
PRIDE:
P0C0R7
PRODB:
PRO_000023767
REFSEQ:
NP_417646
SMR:
P0C0R7
SWISSMODEL:
P0C0R7
UNIPROT:
P0C0R7


Operon      
Name: rlmE-ftsH         
Operon arrangement:
Transcription unit        Promoter
rlmE-ftsH
rlmE-ftsH


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 TSS_3480 3325230 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_3481 3325234 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_3482 3325504 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_3483 3325595 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_3484 3326682 reverse nd [RS-EPT-CBR] [6]
  promoter ftsHp4 3326978 reverse Similarity to the consensus
Read more >
[ICWHO], [RS-EPT-CBR] [6], [7]
  promoter ftsHp1 3327102 reverse Similarity to the consensus
Read more >
[ICWHO] [7]
  promoter TSS_3486 (cluster) 3327294 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [6]
  promoter TSS_3487 3327347 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_3488 3328043 forward nd [RS-EPT-CBR] [6]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Feder M., Pas J., Wyrwicz LS., Bujnicki JM., 2003, Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases., Gene 302(1-2):129-38

 [2] Ishiguro K., Arai T., Suzuki T., 2019, Depletion of S-adenosylmethionine impacts on ribosome biogenesis through hypomodification of a single rRNA methylation., Nucleic Acids Res 47(8):4226-4239

 [3] Porta JM., Jaillet L., 2013, Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation., J Comput Chem 34(3):234-44

 [4] Sergiev PV., Golovina AY., Sergeeva OV., Osterman IA., Nesterchuk MV., Bogdanov AA., Dontsova OA., 2012, How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?, Nucleic Acids Res 40(12):5694-705

 [5] Siibak T., Remme J., 2010, Subribosomal particle analysis reveals the stages of bacterial ribosome assembly at which rRNA nucleotides are modified., RNA 16(10):2023-32

 [6] 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.

 [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


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