RegulonDB RegulonDB 10.10: Gene Form
   

dbpA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dbpA ttcA ynaL TSS_1770 TSS_1770 dbpAp2 dbpAp2

Gene      
Name: dbpA    Texpresso search in the literature
Synonym(s): ECK1340, EG10210, b1343, rhlC
Genome position(nucleotides): 1409511 --> 1410884 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.97
External database links:  
ASAP:
 ABE-0004511
CGSC:
 32058
ECHOBASE:
 EB0206
ECOLIHUB:
 dbpA
OU-MICROARRAY:
 b1343
STRING:
 511145.b1343
COLOMBOS: dbpA


Product      
Name: ATP-dependent RNA helicase DbpA
Synonym(s): ATP-dependent RNA helicase, specific for 23S rRNA, DbpA, RhlC
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 49.188
Isoelectric point: 7.761
Motif(s):
 
Type Positions Sequence
153 -> 156 DEAD
154 -> 154 E
331 -> 331 R
3 -> 31 AFSTLNVLPPAQLTNLNELGYLTMTPVQA
34 -> 205 LPAILAGKDVRVQAKTGSGKTAAFGLGLLQQIDASLFQTQALVLCPTRELADQVAGELRRLARFLPNTKILTLCGGQPFGMQRDSLQHAPHIIVATPGRLLDHLQKGTVSLDALNTLVMDEADRMLDMGFSDAIDDVIRFAPASRQTLLFSATWPEAIAAISGRVQRDPLAI

 
Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0004386 - helicase activity
GO:0016787 - hydrolase activity
GO:0016887 - ATP hydrolysis activity
GO:0003723 - RNA binding
GO:0000166 - nucleotide binding
GO:0003724 - RNA helicase activity
GO:0005524 - ATP binding
GO:0019843 - rRNA binding
GO:0043531 - ADP binding
GO:0034458 - 3'-5' RNA helicase activity
GO:0033677 - DNA/RNA helicase activity
biological_process GO:0042254 - ribosome biogenesis
GO:0000027 - ribosomal large subunit assembly
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [1] Bradley MJ., et al., 2012
[2] Fuller-Pace FV., et al., 1993
[3] Kaminker I., et al., 2015
[4] Lopez-Ramirez V., et al., 2011
[5] Nicol SM., et al., 1995
[6] Sharpe Elles LM., et al., 2009
External database links:  
ECOCYC:
 EG10210-MONOMER
ECOLIWIKI:
 b1343
INTERPRO:
 IPR028619
INTERPRO:
 IPR027417
INTERPRO:
 IPR014014
INTERPRO:
 IPR014001
INTERPRO:
 IPR012677
INTERPRO:
 IPR011545
INTERPRO:
 IPR005580
INTERPRO:
 IPR001650
INTERPRO:
 IPR000629
MODBASE:
 P21693
PFAM:
 PF03880
PFAM:
 PF00271
PFAM:
 PF00270
PRIDE:
 P21693
PRODB:
 PRO_000022405
PROSITE:
 PS51194
PROSITE:
 PS51192
PROSITE:
 PS51195
PROSITE:
 PS00039
REFSEQ:
 NP_415859
SMART:
 SM00487
SMART:
 SM00490
SMR:
 P21693
UNIPROT:
 P21693


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 dbpAp2 1409338 forward nd [ICWHO] [7]
  promoter TSS_1770 1411438 reverse nd [RS-EPT-CBR] [8]


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] Bradley MJ., De La Cruz EM., 2012, Analyzing ATP utilization by DEAD-Box RNA helicases using kinetic and equilibrium methods., Methods Enzymol 511:29-63

 [2] Fuller-Pace FV., Nicol SM., Reid AD., Lane DP., 1993, DbpA: a DEAD box protein specifically activated by 23s rRNA., EMBO J 12(9):3619-26

 [3] Kaminker I., Goldfarb D., 2015, ATPase site configuration of the RNA helicase DbpA probed by ENDOR spectroscopy., Methods Mol Biol 1259:137-64

 [4] Lopez-Ramirez V., Alcaraz LD., Moreno-Hagelsieb G., Olmedo-Alvarez G., 2011, Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins., J Mol Evol 72(4):413-31

 [5] Nicol SM., Fuller-Pace FV., 1995, The "DEAD box" protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA., Proc Natl Acad Sci U S A 92(25):11681-5

 [6] Sharpe Elles LM., Sykes MT., Williamson JR., Uhlenbeck OC., 2009, A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit., Nucleic Acids Res 37(19):6503-14

 [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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