DbpA: a DEAD box protein specifically activated by 23s rRNA.

Fuller-Pace, FV; Nicol, Samantha M.; Reid, A.D.; Lane, David P.

doi:10.1002/j.1460-2075.1993.tb06035.x

Cited by 143 publications

(125 citation statements)

References 25 publications

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“…Although different unwinding activities of DEAD box proteins for duplexes with 59-or 39-single stranded overhangs have been reported, this 'directionality' possibly reflects differences in unwinding that depend on the relative orientation of the DEAD box protein with regard to the target region. For example, the Cterminal domain of DbpA recognizes a hairpin in ribosomal 23S rRNA and the helicase core unwinds an adjacent helix (Fuller-Pace et al, 1993;Diges and Uhlenbeck, 2001;Tsu et al, 2001). Unwinding efficiencies depend on the position of the helix relative to the hairpin (Diges and Uhlenbeck, 2005).…”

Section: Characteristics Of Rna Helicase Substratesmentioning

confidence: 99%

The mechanism of ATP-dependent RNA unwinding by DEAD box proteins

Hilbert

Karow²,

Klostermeier³

2009

BCHM

140

171

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DEAD box proteins catalyze the ATP-dependent unwinding of double-stranded RNA (dsRNA). In addition, they facilitate protein displacement and remodeling of RNA or RNA/protein complexes. Their hallmark feature is local destabilization of RNA duplexes. Here, we summarize current data on the DEAD box protein mechanism and present a model for RNA unwinding that integrates recent data on the effect of ATP analogs and mutations on DEAD box protein activity. DEAD box proteins share a conserved helicase core with two flexibly linked RecAlike domains that contain all helicase signature motifs. Variable flanking regions contribute to substrate binding and modulate activity. In the presence of ATP and RNA, the helicase core adopts a compact, closed conformation with extensive interdomain contacts and high affinity for RNA. In the closed conformation, the RecA-like domains form a catalytic site for ATP hydrolysis and a continuous RNA binding site. A kink in the backbone of the bound RNA locally destabilizes the duplex. Rearrangement of this initial complex generates a hydrolysisand unwinding-competent state. From this complex, the first RNA strand can dissociate. After ATP hydrolysis and phosphate release, the DEAD box protein returns to a low-affinity state for RNA. Dissociation of the second RNA strand and reopening of the cleft in the helicase core allow for further catalytic cycles.

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Section: Characteristics Of Rna Helicase Substratesmentioning

confidence: 99%

The mechanism of ATP-dependent RNA unwinding by DEAD box proteins

Hilbert

Karow²,

Klostermeier³

2009

BCHM

140

171

View full text Add to dashboard Cite

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“…The binding reactions included in vitro translated 35 S-labeled protein and 10 g of RNA resin in 0.5 ml of binding buffer (10 mM HEPES, pH 7.5, 100 mM NaCl, 2 mM MgCl 2 , 0.5% Triton X-100, and 0.1 mg/ml bovine serum albumin) and was incubated for 30 min with rotating at 4°C. The beads were washed three times with ice-cold binding buffer.…”

Section: Amino Acid Sequence Analysis By Lc/ms/ms-followingmentioning

confidence: 99%

“…The expression levels of GFP fusion proteins and the bound FLAG-DDX1 represented in the lower panels are from Western blotting. B, by GST pull-down assay, the in vitro translated 35 Slabeled DDX1 were incubated with GSH beads that were prebound with GST (lane 2) or various lengths of GST-hnRNP K (lanes 3-7). After washing, the bound proteins retained on the beads were analyzed by SDS-PAGE and autoradiography.…”

Section: Ddx1 Interacts With Poly(a) Rna-mentioning

confidence: 99%

An RNA Helicase, DDX1, Interacting with Poly(A) RNA and Heterogeneous Nuclear Ribonucleoprotein K

Chen

Lin

Tsay

et al. 2002

Journal of Biological Chemistry

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Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a multifunctional protein known to be involved in the regulation of transcription, translation, nuclear transport, and signal transduction. To systematically obtain insight into mechanisms of hnRNP K activities, we set out to identify protein factors that interact with hnRNP K by using glutathione S-transferase-hnRNP K affinity chromatography followed by liquid chromatography/mass spectrometry/mass spectrometry analysis. Several partner proteins in the K562 cell lysates were identified through this method. One of them is a DEAD box-containing putative RNA helicase, DDX1. In vitro binding and co-immunoprecipitation studies confirmed the protein-protein interaction between hnRNP K with DDX1, and the region spanning amino acids 1-276 of hnRNP K is apparently responsible for its physical interaction with DDX1. Interestingly, their interaction was disrupted by the addition of poly(C), poly(A), and poly(U) RNA substrates. We found that DDX1 was a homopolymeric poly(A) RNA-binding protein. On the other hand, the ATPase activity of the purified recombinant DDX1 protein was stimulated by these homopolymeric RNAs and yeast total RNA but not by DNA. Moreover, the immunoprecipitated DDX1 complex but not purified DDX1 can unwind double-stranded RNA having singlestranded poly(A) overhangs.The hnRNP K 1 protein has been identified as a component of the heterogeneous nuclear ribonucleoprotein complexes. These hnRNP proteins bind pre-mRNAs directly and appear to facilitate various stages of mRNA biogenesis (1-3). hnRNP K can bind to RNA and single-stranded or double-stranded DNA. The nucleic acid binding activity of hnRNP K is mediated by three repeats of motifs termed the K homology domain, which consists of 65-70 residues (4). It contains both classical nuclear localization signal and the K nuclear shuttling domain that allow the protein to shuttle between nucleus and cytoplasm (5). hnRNP K appears to be involved in transcriptional regulation as exemplified by its binding to a C-rich sequence (the CT element) within the human c-myc promoter and subsequent activation of c-myc expression (6 -8). Additionally, its association with CCAAT/enhancer-binding protein ␤ results in the repression of CCAAT/enhancer-binding protein ␤ target genes (9). hnRNP K was also reported to bind 3Ј end of 15-lipoxygenase, and HPV 16 L2 mRNA was reported to trigger translation inhibition (10, 11). Moreover, direct protein-protein interactions between hnRNP K and some proto-oncogene products serve as clear evidence that hnRNP K acts as a docking platform to facilitate molecular interactions within signal transduction cascades (12-16).Modulation of RNA structure is an essential step in many fundamental cellular processes, including RNA synthesis, splicing, export, turnover, and translation. Recently, an increasing number of RNA helicases from different organisms, ranging from bacteria to yeast, human, and virus, has been identified (17, 18). DEAD box proteins are a family of putative RNA helicases t...

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“…Extensive and beautiful work has pinpointed a CsdA function to the biogenesis of the 50S subunit (Iost and Dreyfus, 2006). The DbpA protein is famous for its requirement for a specific RNA substrate for efficient ATP hydrolysis (Fuller-Pace et al, 1993). Indeed, this DEAD-box protein is exclusively and heavily stimulated in its activity by the hairpin h92 from the 23S rRNA (Diges and Uhlenbeck, 2001;Nicol and Fuller-Pace, 1995).…”

Section: Introductionmentioning

confidence: 99%