Interaction of the Escherichia coli DEAD box protein DbpA with 23 S ribosomal RNA

• Published in: Journal of molecular biology Vol. 292; no. 4; pp. 771 - 778
• Main Authors: Pugh, G.E, Nicol, S.M, Fuller-Pace, F.V
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.10.1999
• Subjects: 23 S rRNA; Adenosine Triphosphatases - metabolism; Amino Acid Motifs; ATPase; Bacterial Proteins - metabolism; Base Sequence; Binding Sites; DbpA; DEAD-box protein; DEAD-box RNA Helicases; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli Proteins; Hydrolysis; Molecular Sequence Data; Mutation; Nucleic Acid Conformation; RNA binding; RNA Helicases - metabolism; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Ribosomal, 23S - chemistry; RNA, Ribosomal, 23S - genetics; RNA, Ribosomal, 23S - metabolism; RNA-Binding Proteins - metabolism; Substrate Specificity; DEAD-box protein; 23 S rRNA; ATPase; RNA binding; DbpA
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.1999.3112

The Escherichia coli DEAD box protein DbpA is unique among the DEAD box family in that its ATPase activity is specifically stimulated by bacterial 23 S ribosomal RNA. We have analysed the interaction between DbpA and a specific region within 23 S rRNA (namely nucleotides 2508–2580) which stimulates full ATPase activity. Using electrophoretic mobility shift assays we show that DbpA binds to this “specific” region with greater efficiency than to other regions of 23 S rRNA, and is not competed off by a non-specific RNA or a mutant RNA in which one of the stem-loops has been disrupted. These data suggest that the secondary structure within this region of 23 S rRNA is important for its recognition and binding by DbpA. We have also examined the ability of DbpA to unwind RNA and show that the purified protein does not behave as an RNA helicase in vitro with the substrates tested.