Falcon deep research report on DBP5 (Saccharomyces cerevisiae Dbp5/Rat8, UniProt P20449)
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Dbp5/Rat8 is an essential DEAD-box ATP-dependent RNA helicase / RNA-dependent
ATPase that acts at the cytoplasmic face of the nuclear pore complex (NPC)
and is orthologous to metazoan DDX19.
"The literature summarized here is specifically for **Dbp5** (alias **Rat8**) from *Saccharomyces cerevisiae* (S288c), an essential **DEAD-box ATP-dependent RNA helicase/RNA-dependent ATPase** at the nuclear pore complex (NPC), orthologous to metazoan **DDX19**."
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The core activity of Dbp5 is RNA-dependent ATP hydrolysis coupled to
nucleotide-state-dependent conformational cycling, enabling binding and
remodeling of RNA-protein complexes (RNPs) rather than long-range processive
duplex unwinding; this remodeling is often described as an RNPase activity.
"Dbp5 is a DEAD-box RNA helicase-family protein whose core activity is **RNA-dependent ATP hydrolysis** coupled to **nucleotide-state–dependent conformational cycling**, enabling binding and remodeling of RNA–protein complexes (RNPs) rather than long-range processive duplex unwinding. In the export context, this remodeling function is often described as an **RNPase** activity acting on messenger RNPs at the NPC"
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mRNP remodeling by Dbp5 at the cytoplasmic NPC face removes export-associated
factors such as Mex67-Mtr2 and Nab2 from exported mRNA, enforcing directionality.
"The mechanistic focus is on Dbp5-driven removal of export-associated factors such as **Mex67–Mtr2** (major mRNA export receptor) and **Nab2** (poly(A) RNA-binding/export factor), thereby enforcing directionality and enabling cytoplasmic fate decisions"
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Directionality of export is established at the cytoplasmic NPC face, where Dbp5
activity promotes dissociation of export factors so the mRNP cannot re-enter
the nucleus using the same export-binding interactions.
"Directionality is established at the **cytoplasmic NPC face**, where Dbp5 activity promotes dissociation of export factors from the mRNP so that the particle **cannot re-enter the nucleus using the same export-binding interactions**"
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Dbp5 catalyzes RNA-dependent ATP hydrolysis (ATP to ADP + Pi), with the
remodeling function associated with conformational changes across its
nucleotide cycle.
"Dbp5 catalyzes **ATP hydrolysis (ATP → ADP + Pi)** in an RNA-dependent manner, with its remodeling function associated with conformational changes across its nucleotide cycle"
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Gle1 bound to inositol hexakisphosphate (IP6) activates the Dbp5 ATPase and
promotes localized mRNP remodeling and directionality; the same module is
required for proper translation termination.
"Alcázar-Román et al. (JBC 2010-05-28, https://doi.org/10.1074/jbc.M109.082370) describe Gle1 and IP6 as essential for mRNA export by **activating Dbp5 ATPase** and promoting localized mRNP remodeling and directionality; they also report that the same module is required for **proper translation termination**"
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Nup159 tethers Dbp5 to NPC cytoplasmic filaments and primarily facilitates
ADP release / recycling, enabling additional rounds of remodeling; ADP binding
alone is sufficient to drive in vitro Nab2-RNP remodeling.
"Noble et al. (Genes & Dev. 2011-05, https://doi.org/10.1101/gad.2040611) conclude that “a primary role for Nup159 in the Dbp5 cycle is to facilitate ADP release,” and show that ADP binding alone is sufficient to drive in vitro remodeling of Nab2-RNPs under their assay conditions"
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Nup42 enhances Gle1-dependent stimulation of the RNA-dependent Dbp5 ATPase
and supports formation of a Nup42-CTD/Gle1-CTD/Dbp5 trimeric complex in the
presence of IP6.
"Adams et al. (Traffic 2017-10, https://doi.org/10.1111/tra.12526) report that Nup42/hNup42 enhances Gle1 stimulation of the RNA-dependent Dbp5/DDX19B ATPase, and that a **nup42-CTD/gle1-CTD/Dbp5 trimeric complex forms in the presence of IP6**"
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Dbp5 association with NPCs is highly dynamic, with an average residence time
of approximately 0.8 s reported by FRAP in yeast.
"Dbp5 association with NPCs is highly dynamic, with **~0.8 s** average residence time reported by FRAP in yeast"
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Dbp5 directly binds tRNA in vitro (Kd ~150 nM Phe tRNA, ~130 nM mixed tRNA),
but tRNA/dsRNA alone does not stimulate its ATPase; instead it synergizes with
Gle1/InsP6 to fully activate Dbp5.
"Dbp5 binds tRNA in vitro with **Kd ~150 nM** (Phe tRNA) and **~130 nM** (mixed tRNA) (Rajan et al., eLife 2024-01, https://doi.org/10.7554/elife.89835)."
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tRNA (or dsRNA poly(I:C)) alone does not stimulate Dbp5 ATPase activity, unlike
a typical ssRNA activator (poly(A)); tRNA/dsRNA synergizes with Gle1/InsP6 to
fully activate Dbp5 to a level comparable with ssRNA activation.
"**tRNA (or dsRNA poly(I:C)) alone does not stimulate Dbp5 ATPase activity**, unlike a typical ssRNA activator (poly(A)). However, **tRNA/dsRNA synergizes with Gle1/InsP6 to fully activate Dbp5**, reaching ~**1.03 ± 0.04 ATP/s** (mixed tRNA with Gle1/InsP6) comparable to ssRNA activation (~**1.11 ± 0.07 ATP/s**)"
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Rajan et al. provide genetic and biochemical evidence that Dbp5 functions in
tRNA export in a pathway parallel to canonical exporters (Los1-independent),
with Gle1 supporting pre-tRNA export.
"Rajan et al. (eLife 2024-01) provide genetic and biochemical evidence that Dbp5 functions in tRNA export in a pathway parallel to canonical exporters:"
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Querl & Krebber (2023) review evidence that Dbp5 functions in translation
termination via a model in which Dbp5 delivers eRF1 to terminating ribosomes
and prevents premature eRF1-eRF3 interactions, thereby reducing readthrough.
"Querl & Krebber (Biological Chemistry, published online 2023-07-13, https://doi.org/10.1515/hsz-2023-0130) review evidence that Dbp5 functions in **translation termination**, including a mechanistic model where Dbp5 delivers **eRF1** to terminating ribosomes and prevents premature eRF1–eRF3 interactions, thereby reducing readthrough"
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Querl & Krebber (2023) summarize a model in which Dbp5 contributes to no-go
decay (NGD) and non-stop decay (NSD) by delivering rescue factors Dom34/Hbs1
to stalled ribosomes.
"Querl & Krebber (2023) summarize a model in which Dbp5 contributes to no-go decay (NGD) and non-stop decay (NSD) by delivering rescue factors **Dom34/Hbs1** to stalled ribosomes; subsequent hydrolysis steps coordinate rescue and transcript clearance"
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Recent synthesis places Dbp5 in pre-ribosomal subunit export, with a model
where Dbp5 binds Mex67 on pre-ribosomal particles in the cytoplasm to capture
translocating subunits; this role may be less dependent on canonical helicase
remodeling than mRNA export.
"Recent synthesis also places Dbp5 in pre-ribosomal export, with a model distinct from canonical mRNA remodeling:"