RegulonDB RegulonDB 10.9: Gene Form
   

rsmA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

surA pdxA rsmA apaG TSS_93 TSS_93 TSS_92 TSS_92 TSS_91 TSS_91 TSS_90 TSS_90 rsmAp rsmAp TSS_89 TSS_89 TSS_88 TSS_88 TSS_87 (cluster) TSS_87 (cluster) TSS_86 TSS_86 apaGp apaGp TSS_84 TSS_84 apaHp4 apaHp4

Gene      
Name: rsmA    Texpresso search in the literature
Synonym(s): ECK0052, EG10523, b0051, ksgA
Genome position(nucleotides): 51609 <-- 52430 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.04
External database links:  
ASAP:
ABE-0000175
CGSC:
583
ECHOBASE:
EB0518
ECOLIHUB:
ksgA
OU-MICROARRAY:
b0051
STRING:
511145.b0051
COLOMBOS: rsmA


Shine dalgarno      
Sequence: aaaatgattgTTAACAcccAAT


Product      
Name: 16S rRNA m62A1518,m62A1519 dimethyltransferase
Synonym(s): KsgA, RsmA, rRNA small subunit methyltransferase A, ribosomal RNA small subunit methyltransferase A
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.42
Isoelectric point: 8.229
Motif(s):
 
Type Positions Sequence
9 -> 265 HLARKRFGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLA
66 -> 66 E
2 -> 273 NNRVHQGHLARKRFGQNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAENAPLQES

 

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:0008649 - rRNA methyltransferase activity
GO:0003723 - RNA binding
GO:0003729 - mRNA binding
GO:0003690 - double-stranded DNA binding
GO:0016433 - rRNA (adenine) methyltransferase activity
GO:0000179 - rRNA (adenine-N6,N6-)-dimethyltransferase activity
GO:0043024 - ribosomal small subunit binding
GO:0052908 - 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
biological_process GO:0000154 - rRNA modification
GO:0031167 - rRNA methylation
GO:0046677 - response to antibiotic
GO:0006364 - rRNA processing
GO:0032259 - methylation
GO:0030490 - maturation of SSU-rRNA
GO:0000028 - ribosomal small subunit assembly
GO:0070475 - rRNA base methylation
Note(s): Note(s): ...[more].
Reference(s): [1] Andresson OS., et al., 1980
[2] Andresson OS., et al., 1980
[3] Chen J., et al., 2002
[4] Helser TL., et al., 1971
[5] Helser TL., et al., 1972
[6] Kang TM., et al., 2012
[7] O'Farrell HC., et al., 2012
[8] Pulicherla N., et al., 2009
[9] Roa BB., et al., 1989
[10] Sparling PF., et al., 1973
[11] van Buul CP., et al., 1985
[12] van Gemen B., et al., 1987
External database links:  
ECOCYC:
EG10523-MONOMER
ECOLIWIKI:
b0051
INTERPRO:
IPR023165
INTERPRO:
IPR029063
INTERPRO:
IPR020598
INTERPRO:
IPR020596
INTERPRO:
IPR011530
INTERPRO:
IPR001737
MODBASE:
P06992
PANTHER:
PTHR11727
PDB:
1QYR
PDB:
4ADV
PDB:
3TPZ
PFAM:
PF00398
PRIDE:
P06992
PRODB:
PRO_000023881
PROSITE:
PS51689
PROSITE:
PS01131
REFSEQ:
NP_414593
SMART:
SM00650
SMR:
P06992
UNIPROT:
P06992


Operon      
Name: lptD-surA-pdxA-rsmA-apaGH         
Operon arrangement:
Transcription unit        Promoter
apaGH
rsmA-apaGH
imp
imp
imp-surA-pdxA
pdxA-rsmA
pdxA-rsmA-apaGH
surA-pdxA-rsmA-apaGH


Transcriptional Regulation      
Display Regulation             
Activated by: Fis


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 apaHp4 51293 reverse Similarity to the consensus
Read more >
[ICWHO] [13]
  promoter TSS_84 51998 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_86 52194 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_87 (cluster) 52478 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [14]
  promoter TSS_88 52548 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_89 52587 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_90 53904 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_91 54275 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_92 54363 reverse nd [RS-EPT-CBR] [14]
  promoter TSS_93 54605 reverse nd [RS-EPT-CBR] [14]


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] Andresson OS., Davies JE., 1980, Genetic organization and restriction enzyme cleavage map of the ksgA-pdxA region of the Escherichia coli chromosome., Mol Gen Genet 179(1):211-6

 [2] Andresson OS., Davies JE., 1980, Isolation and characterization of lambda transducing phages for the E. coli genes ksgA and pdxA., Mol Gen Genet 179(1):201-9

 [3] Chen J., Acton TB., Basu SK., Montelione GT., Inouye M., 2002, Enhancement of the solubility of proteins overexpressed in Escherichia coli by heat shock., J Mol Microbiol Biotechnol 4(6):519-24

 [4] Helser TL., Davies JE., Dahlberg JE., 1971, Change in methylation of 16S ribosomal RNA associated with mutation to kasugamycin resistance in Escherichia coli., Nat New Biol 233(35):12-4

 [5] Helser TL., Davies JE., Dahlberg JE., 1972, Mechanism of kasugamycin resistance in Escherichia coli., Nat New Biol 235(53):6-9

 [6] Kang TM., Yuan J., Nguyen A., Becket E., Yang H., Miller JH., 2012, The aminoglycoside antibiotic kanamycin damages DNA bases in Escherichia coli: caffeine potentiates the DNA-damaging effects of kanamycin while suppressing cell killing by ciprofloxacin in Escherichia coli and Bacillus anthracis., Antimicrob Agents Chemother 56(6):3216-23

 [7] O'Farrell HC., Rife JP., 2012, Staphylococcus aureus and Escherichia coli have disparate dependences on KsgA for growth and ribosome biogenesis., BMC Microbiol 12:244

 [8] Pulicherla N., Pogorzala LA., Xu Z., O Farrell HC., Musayev FN., Scarsdale JN., Sia EA., Culver GM., Rife JP., 2009, Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases., J Mol Biol 391(5):884-93

 [9] Roa BB., Connolly DM., Winkler ME., 1989, Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of Escherichia coli K-12., J Bacteriol 171(9):4767-77

 [10] Sparling PF., Ikeya Y., Elliot D., 1973, Two genetic loci for resistance to kasugamycin in Escherichia coli., J Bacteriol 113(2):704-10

 [11] van Buul CP., van Knippenberg PH., 1985, Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA., Gene 38(1-3):65-72

 [12] van Gemen B., Koets HJ., Plooy CA., Bodlaender J., Van Knippenberg PH., 1987, Characterization of the ksgA gene of Escherichia coli determining kasugamycin sensitivity., Biochimie 69(8):841-8

 [13] 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

 [14] 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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