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DEAD-box helicases as integrators of RNA, nucleotide and protein binding
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title
DEAD-box helicases as integrators of RNA, nucleotide and protein binding
(English)
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PubMed
author
Eckhard Jankowsky
series ordinal
2
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author name string
Andrea A. Putnam
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1
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Crossref
language of work or name
English
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PubMed
publication date
August 2013
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PubMed
published in
Biochimica et Biophysica Acta
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PubMed
volume
1829
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PubMed
issue
8
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PubMed
page(s)
884-93
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PubMed
cites work
DEAD-box proteins as RNA helicases and chaperones
1 reference
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PubMed Central
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21 March 2017
RNA helicases at work: binding and rearranging
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PubMed Central
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21 March 2017
SF1 and SF2 helicases: family matters
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PubMed Central
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21 March 2017
Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation
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PubMed Central
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21 March 2017
ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
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21 March 2017
Biochemical characterization of the ATPase and helicase activity of UAP56, an essential pre-mRNA splicing and mRNA export factor
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PubMed Central
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21 March 2017
Dead-box proteins: a family affair--active and passive players in RNP-remodeling
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21 March 2017
The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA
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21 March 2017
Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54
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21 March 2017
CELLULAR DNA REPLICASES: Components and Dynamics at the Replication Fork
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21 March 2017
The highly related DEAD box RNA helicases p68 and p72 exist as heterodimers in cells
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PubMed Central
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21 March 2017
Helicase structure and mechanism
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21 March 2017
Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase
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21 March 2017
Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p
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21 March 2017
A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export
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21 March 2017
Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop
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21 March 2017
Structure of the Yeast DEAD Box Protein Mss116p Reveals Two Wedges that Crimp RNA
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21 March 2017
Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B
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21 March 2017
The DEXD/H-box RNA Helicase DDX19 Is Regulated by an -Helical Switch
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21 March 2017
A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility
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21 March 2017
Mechanism of ATP turnover inhibition in the EJC
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21 March 2017
Crystal structure of conserved domains 1 and 2 of the human DEAD-box helicase DDX3X in complex with the mononucleotide AMP
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21 March 2017
The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding
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21 March 2017
The DEAD-box RNA helicase Dbp2 connects RNA quality control with repression of aberrant transcription
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21 March 2017
RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex
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21 March 2017
The DEAD-box protein Ded1 modulates translation by the formation and resolution of an eIF4F-mRNA complex
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21 March 2017
The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex
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21 March 2017
Control of ATP homeostasis during the respiro-fermentative transition in yeast
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21 March 2017
Differential RNA-dependent ATPase activities of four rRNA processing yeast DEAD-box proteins
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21 March 2017
Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity
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21 March 2017
Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export
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21 March 2017
Inositol hexakisphosphate and Gle1 activate the DEAD-box protein Dbp5 for nuclear mRNA export
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21 March 2017
Discriminatory RNP remodeling by the DEAD-box protein DED1.
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21 March 2017
ATP- and ADP-dependent modulation of RNA unwinding and strand annealing activities by the DEAD-box protein DED1.
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21 March 2017
The Putative RNA Helicase Dbp4p Is Required for Release of the U14 snoRNA from Preribosomes in Saccharomyces cerevisiae
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21 March 2017
Ded1p, a DEAD-box protein required for translation initiation in Saccharomyces cerevisiae, is an RNA helicase
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21 March 2017
Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA
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21 March 2017
The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity
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21 March 2017
Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA.
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21 March 2017
The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA.
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21 March 2017
The helicase DDX41 recognizes the bacterial secondary messengers cyclic di-GMP and cyclic di-AMP to activate a type I interferon immune response
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21 March 2017
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa
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7 April 2017
The DEAD-box protein family of RNA helicases
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7 April 2017
Multiple binding of repressed mRNAs by the P-body protein Rck/p54.
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28 September 2017
Specific domains in yeast translation initiation factor eIF4G strongly bias RNA unwinding activity of the eIF4F complex toward duplexes with 5'-overhangs
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28 September 2017
ATP utilization and RNA conformational rearrangement by DEAD-box proteins
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28 September 2017
Arginine methylation of RNA-binding proteins regulates cell function and differentiation
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28 September 2017
From unwinding to clamping - the DEAD box RNA helicase family
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28 September 2017
Single-molecule studies reveal that DEAD box protein DDX1 promotes oligomerization of HIV-1 Rev on the Rev response element
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28 September 2017
Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail
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28 September 2017
Synergistic activation of eIF4A by eIF4B and eIF4G.
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28 September 2017
eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism
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28 September 2017
An ancient anion-binding structural module in RNA and DNA helicases
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28 September 2017
DEAD-box helicases: posttranslational regulation and function
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28 September 2017
Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA.
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28 September 2017
The mechanism of ATP-dependent RNA unwinding by DEAD box proteins
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28 September 2017
RecQ helicases: multifunctional genome caretakers
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28 September 2017
A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN.
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28 September 2017
DEAD-box proteins can completely separate an RNA duplex using a single ATP.
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28 September 2017
Interactions between eIF4AI and its accessory factors eIF4B and eIF4H
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28 September 2017
Translocation and unwinding mechanisms of RNA and DNA helicases
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28 September 2017
Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs
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28 September 2017
A conserved phenylalanine of motif IV in superfamily 2 helicases is required for cooperative, ATP-dependent binding of RNA substrates in DEAD-box proteins
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28 September 2017
The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA
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28 September 2017
Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase
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28 September 2017
RNA 1997-2007: a remarkable decade of discovery
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28 September 2017
Anti-inflammatory lipid mediator 15d-PGJ2 inhibits translation through inactivation of eIF4A.
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28 September 2017
Modulation of transcriptional activity of the DEAD-box family of RNA helicases, p68 (Ddx5) and DP103 (Ddx20), by SUMO modification
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28 September 2017
DEAD-box proteins unwind duplexes by local strand separation
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28 September 2017
Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone
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28 September 2017
SUMO modification of the DEAD box protein p68 modulates its transcriptional activity and promotes its interaction with HDAC1.
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28 September 2017
Nonspecific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone
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28 September 2017
P68 RNA helicase mediates PDGF-induced epithelial mesenchymal transition by displacing Axin from beta-catenin
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28 September 2017
Remodeling of ribonucleoprotein complexes with DExH/D RNA helicases
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28 September 2017
DExD/H box RNA helicases: multifunctional proteins with important roles in transcriptional regulation
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28 September 2017
The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
Hydrodynamic characterization of the DEAD-box RNA helicase DbpA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
Crystal structure of the human ATP-dependent splicing and export factor UAP56.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
The active form of Xp54 RNA helicase in translational repression is an RNA-mediated oligomer
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
A novel domain within the DEAD-box protein DP103 is essential for transcriptional repression and helicase activity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
Modulation of the helicase activity of eIF4A by eIF4B, eIF4H, and eIF4F.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
Rearrangement of structured RNA via branch migration structures catalysed by the highly related DEAD-box proteins p68 and p72.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
Further characterization of the helicase activity of eIF4A. Substrate specificity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for sub2, an essential spliceosomal ATPase
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
The "DEAD box" protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
DbpA: a DEAD box protein specifically activated by 23s rRNA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 September 2017
Mechanism of Mss116 ATPase reveals functional diversity of DEAD-Box proteins
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
31 May 2018
Motif III in superfamily 2 "helicases" helps convert the binding energy of ATP into a high-affinity RNA binding site in the yeast DEAD-box protein Ded1.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
31 May 2018
Unwinding by local strand separation is critical for the function of DEAD-box proteins as RNA chaperones
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
31 May 2018
Function of the C-terminal domain of the DEAD-box protein Mss116p analyzed in vivo and in vitro
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
31 May 2018
ATP-dependent recruitment of export factor Aly/REF onto intronless mRNAs by RNA helicase UAP56
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
31 May 2018
DEAD-box-protein-assisted RNA structure conversion towards and against thermodynamic equilibrium values
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
31 May 2018
Conformational changes of DEAD-box helicases monitored by single molecule fluorescence resonance energy transfer.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
Duplex unwinding with DEAD-box proteins.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
The DEAD-box protein Dbp5 controls mRNA export by triggering specific RNA:protein remodeling events
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
Equilibrium and kinetic analysis of nucleotide binding to the DEAD-box RNA helicase DbpA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
Studies on three E. coli DEAD-box helicases point to an unwinding mechanism different from that of model DNA helicases
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
Protein displacement by DExH/D "RNA helicases" without duplex unwinding
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
The DExH protein NPH-II is a processive and directional motor for unwinding RNA
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3661757
retrieved
28 November 2018
Structural domains involved in the RNA folding activity of RNA helicase II/Gu protein
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23416748
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23416748
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
RNA-stimulated ATPase activity of eukaryotic initiation factors
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23416748
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23416748
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Glucose repression/derepression in budding yeast: SNF1 protein kinase is activated by phosphorylation under derepressing conditions, and this correlates with a high AMP:ATP ratio
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23416748
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23416748
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
RNA structural rearrangement via unwinding and annealing by the cyanobacterial RNA helicase, CrhR
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/23416748
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1016/J.BBAGRM.2013.02.002
0 references
PMC publication ID
3661757
1 reference
stated in
PubMed
PubMed publication ID
23416748
1 reference
stated in
PubMed
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