Affinage

DDX23

Probable ATP-dependent RNA helicase DDX23 · UniProt Q9BUQ8

Length
820 aa
Mass
95.6 kDa
Annotated
2026-06-09
27 papers in source corpus 18 papers cited in narrative 18 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

DDX23 (yeast Prp28) is a DEAD-box RNA helicase that functions at the heart of pre-mRNA splicing as a core component of the U4/U6-U5 tri-snRNP, where its ATPase activity drives the transition from a pre-catalytic pre-B intermediate to the activated spliceosome by remodeling the U1 snRNP/5' splice-site interaction (PMID:27377154, PMID:34035302). Its enzymatic core comprises two RecA-like domains that adopt a wide-open conformation; the human helicase domain is intrinsically catalytically inert in isolation and acquires ATP-binding activity only upon spliceosomal assembly, while the yeast enzyme has measurable RNA-dependent ATPase activity (PMID:25303995, PMID:24914973). Stable tri-snRNP association and integration into the B complex depend on SRPK2-mediated phosphorylation of the metazoan-specific N-terminal RS-like domain (PMID:18425142), a region that also mediates direct binding to SRSF1 and is required for spliceosome incorporation and proper subnuclear localization (PMID:38743621); in yeast, phosphorylated Npl3 serves as the functional counterpart that potentiates Prp28 ATPase activity (PMID:34035302). Beyond canonical splicing, DDX23 maintains genomic stability by resolving transcription-associated R-loops downstream of the SRPK2 phosphorylation axis and through recruitment by Polymerase κ to R-loop loci (PMID:28076779, PMID:41949541), and it promotes Drosha-dependent primary miRNA processing in a manner requiring its helicase activity (PMID:26121981, PMID:26601717). DDX23 has additionally been implicated in antiviral defense as a cytoplasmic dsRNA sensor engaging TRIF/MAVS (PMID:31620127) and in cancer-associated splicing programs (PMID:34966670), though these activities are less fully resolved in the available corpus.

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1994 High

    Established that the DDX23 ortholog Prp28 is functionally required for the first catalytic step of splicing, setting the question of what activates a helicase that appears inactive alone.

    Evidence Protein purification and in vitro splicing/strand-displacement assays in S. cerevisiae

    PMID:7520570

    Open questions at the time
    • No helicase activity detected for purified protein, implying missing activating factors
    • Did not define the RNA substrate remodeled during splicing
  2. 2008 High

    Answered how the metazoan helicase is integrated into the spliceosome by identifying SRPK2 phosphorylation of the RS domain as the requirement for stable tri-snRNP association and B-complex integration.

    Evidence RNAi depletion, immunodepletion/complementation in HeLa nuclear extract, mass spectrometry

    PMID:18425142

    Open questions at the time
    • Did not resolve the structural consequence of phosphorylation on tri-snRNP binding
    • Phosphosite mapping on DDX23 not detailed
  3. 2013 Medium

    Revealed that Prp28 has an early ATP-independent role in commitment complex formation beyond its ATP-dependent activation function, with Prp8 regulating both activities.

    Evidence Genetic suppressor screen and spliceosome assembly assays in S. cerevisiae

    PMID:24231520

    Open questions at the time
    • Molecular basis of the ATP-independent CC2 function unresolved
    • Human relevance of the early function not tested
  4. 2014 High

    Defined the catalytic architecture: crystal structures showed two RecA domains in an open conformation, and biochemistry distinguished active yeast ATPase from a human domain that is inert in isolation but ATP-competent within the assembled spliceosome.

    Evidence X-ray crystallography of yeast and human Prp28, ATPase and nucleotide-binding assays, alanine-scanning mutagenesis

    PMID:24914973 PMID:25303995

    Open questions at the time
    • Structural state of DDX23 within an intact spliceosome not captured
    • Mechanism that switches the human domain from ADP- to ATP-binding within complex unknown
  5. 2015 Medium

    Extended DDX23 function beyond splicing by showing it promotes Drosha-dependent primary miRNA processing in a helicase-activity-dependent manner, conserved from worms to human glioma.

    Evidence Co-IP with Drosha, helicase-domain mutagenesis, knockdown/overexpression and xenografts; C. elegans RNAi with pri-/mature miRNA quantification

    PMID:26121981 PMID:26601717

    Open questions at the time
    • Substrate hand-off between DDX23 and the microprocessor not biochemically reconstituted
    • Whether splicing and miRNA functions use the same molecular activity unclear
  6. 2016 High

    Characterized the pre-catalytic transition by showing an ATPase-deficient human Prp28 stalls a pre-B complex with loosely associated tri-snRNP before U1/5'ss disruption, indicating an ATPase function beyond merely displacing U1.

    Evidence Dominant-negative ATPase mutant, spliceosomal complex purification, electron microscopy, mass spectrometry; ortholog crystal structure confirmation

    PMID:27139834 PMID:27377154

    Open questions at the time
    • The additional ATPase-dependent step beyond U1 displacement not defined
    • Direct RNA target of the remodeling not identified
  7. 2017 High

    Connected the SRPK2-DDX23 phosphorylation axis to genome maintenance, showing phosphorylated DDX23 suppresses R-loops and prevents double-strand breaks downstream of Pol II pausing.

    Evidence siRNA knockdown of SRPK2/DDX23, S9.6 R-loop immunofluorescence, γH2AX, rescue experiments

    PMID:28076779

    Open questions at the time
    • Whether DDX23 unwinds R-loops directly or via splicing not separated
    • Genomic loci of DDX23-dependent R-loop resolution not mapped
  8. 2019 Medium

    Proposed a non-splicing antiviral role in which DDX23 binds cytoplasmic dsRNA and engages TRIF/MAVS to drive NF-κB/IRF3 signaling, restricting viral replication.

    Evidence Poly(I:C) pull-down, Co-IP with TRIF/MAVS, siRNA knockdown, VSV replication and signaling readouts, localization imaging

    PMID:31620127

    Open questions at the time
    • Nuclear-to-cytoplasmic translocation trigger not mechanistically defined
    • Single-lab finding without reciprocal validation of TRIF/MAVS complexes
  9. 2021 Medium

    Refined the activation mechanism by mapping Prp28 contacts to the 5'ss GU and to U1C/Prp8/Brr2/Snu114, and identified phospho-Npl3 as the yeast functional counterpart of the metazoan phospho-N-terminus that stimulates ATPase activity.

    Evidence Co-IP, splicing-dependent crosslinking, in vitro ATPase assays with phospho- vs unphospho-Npl3

    PMID:34035302

    Open questions at the time
    • Structural basis of Npl3-mediated ATPase stimulation unresolved
    • Whether human SRPK2-DDX23 and yeast Npl3-Prp28 are mechanistically equivalent not directly tested
  10. 2024 High

    Established a direct SR-protein partnership, defining the DDX23 N-terminal RS-like domain and SRSF1 RRM1/RS domain as the binding interface and linking this region to spliceosome incorporation and subnuclear localization.

    Evidence BioID proximity labeling/MS, BiFC, in vitro binding assays, deletion mutagenesis with localization imaging

    PMID:38743621

    Open questions at the time
    • Functional consequence of the SRSF1 interaction for specific splicing events not defined
    • Phosphorylation dependence of the SRSF1 interaction not tested
  11. 2025 Medium

    Identified Polymerase κ as a recruiter of DDX23 to chromatin R-loop loci, providing a targeting mechanism for its R-loop resolution activity.

    Evidence BioID and affinity pull-down with LC-MS/MS, Co-IP, S9.6 R-loop immunofluorescence, individual KO/KD

    PMID:41949541

    Open questions at the time
    • Whether DDX23 enzymatically unwinds R-loops at Pol κ sites not shown directly
    • Single-lab study

Open questions

Synthesis pass · forward-looking unresolved questions
  • How DDX23 partitions among its splicing, R-loop, miRNA-processing, and antiviral activities—and whether a single helicase/ATPase activity underlies all of them—remains unresolved.
  • No unified model linking the distinct functions to defined RNA substrates
  • Structure of DDX23 within an active spliceosome or R-loop complex not determined
  • Regulatory switch governing nuclear vs cytoplasmic functions unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140098 catalytic activity, acting on RNA 4 GO:0003723 RNA binding 3 GO:0140657 ATP-dependent activity 3 GO:0016787 hydrolase activity 2
Localization
GO:0005634 nucleus 2 GO:0005829 cytosol 1
Pathway
R-HSA-8953854 Metabolism of RNA 3 R-HSA-73894 DNA Repair 2 R-HSA-168256 Immune System 1
Partners
BRR2DROSHAMAVSPRP8SNU114SRPK2SRSF1TRIF
Complex memberships
Drosha microprocessorU4/U6-U5 tri-snRNPspliceosome (pre-B/B complex)

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2008 SRPK2 phosphorylates the RS domain of human PRP28/DDX23, and this phosphorylation is required for stable association of PRP28 with the U4/U6-U5 tri-snRNP and for tri-snRNP integration into the spliceosomal B complex. SRPK1 is predominantly associated with U1 snRNP, while SRPK2 associates with tri-snRNP. RNAi depletion of SRPK2 causes hypophosphorylation of PRP28 and destabilizes its tri-snRNP association. RNAi depletion in HeLa cells, immunodepletion and complementation assays in nuclear extract, mass spectrometry Nature structural & molecular biology High 18425142
2017 RNA polymerase II pausing initiates a signaling cascade in which SRPK2 phosphorylates DDX23, and phosphorylated DDX23 suppresses R-loops. In the absence of either SRPK2 or DDX23, R-loops accumulate and cause DNA double-strand breaks, revealing a role for DDX23 in maintaining genomic stability downstream of transcription dynamics. RNAi/siRNA knockdown of SRPK2 and DDX23 in human cells, R-loop immunofluorescence (S9.6 antibody), DNA damage markers (γH2AX), rescue experiments Cell reports High 28076779
1994 Yeast Prp28 (ortholog of DDX23) is required for the first step of pre-mRNA splicing in vitro. Prp28 is not a stably associated snRNP protein. Purified Prp28 does not exhibit RNA helicase activity in strand displacement assays, suggesting additional factors are needed for its activation. Protein purification from S. cerevisiae, in vitro splicing assay, strand displacement assay Nucleic acids research High 7520570
2016 ATPase-deficient human Prp28/DDX23 blocks stable tri-snRNP association during B complex formation and stabilizes a novel assembly intermediate (pre-B complex) containing U1, U2, and loosely associated tri-snRNP, stalled before disruption of U1/5' splice-site base pairing. Disruption of the U1/5'ss interaction alone is insufficient to bypass the block, suggesting an additional function for hPrp28 ATPase activity at this stage. Dominant-negative ATPase-deficient hPrp28 mutant expression, spliceosomal complex purification and characterization, electron microscopy structural analysis, mass spectrometry Nature communications High 27377154
2014 Crystal structure of yeast Prp28 (ortholog of DDX23) reveals two RecA-like domains in a wide-open conformation. Prp28 has intrinsic RNA-dependent ATPase activity. Alanine scanning mutagenesis identified essential residues: Asp341/Glu342 (motif II) and Arg527/Arg530 (motif VI) for ATP binding, and Arg476 (motif Va) for RNA binding. Overexpression of ATP-site but not RNA-site defective mutants caused dominant-negative growth defects. X-ray crystallography (crystal structure), in vitro ATPase assay, alanine scanning mutagenesis, in vivo growth assays in S. cerevisiae Nucleic acids research High 25303995
2014 The purified helicase domain of human Prp28/DDX23 binds ADP but not ATP and lacks detectable ATPase activity in isolation; however, within an assembled spliceosomal complex, hPrp28 gains ATP-binding activity. The crystal structure at 2.0 Å shows the helicase domain in a wide-open conformation with a closed P-loop that blocks γ-phosphate binding of ATP. X-ray crystallography (2.0 Å crystal structure of hPrp28ΔN), nucleotide-binding assays with purified protein and spliceosomal complex Acta crystallographica. Section D, Biological crystallography High 24914973
2015 DDX23 promotes miR-21 biogenesis at the post-transcriptional level by facilitating primary-to-precursor (pri-to-pre) processing of miR-21 through direct interaction with the Drosha microprocessor. Mutagenesis demonstrated that the helicase activity of DDX23 is essential for this processing step. Co-immunoprecipitation, knockdown and overexpression in glioma cells, miRNA processing assays, helicase domain mutagenesis, xenograft mouse models Brain : a journal of neurology Medium 26121981
2015 C. elegans DDX-23 (ortholog of DDX23) is required for primary miRNA processing: knockdown causes accumulation of pri-let-7 and reduction of mature let-7, lin-4, miR-48, miR-84, miR-241, and lsy-6, indicating DDX-23 acts at the level of Drosha-mediated pri-miRNA cleavage. RNAi knockdown in C. elegans, miRNA quantification (mature and primary forms), genetic sensitized background (let-7(mg279)) Developmental biology Medium 26601717
2013 In yeast, Prp28 has an early ATP-independent function in commitment complex 2 (CC2) formation in addition to its known ATP-dependent role in spliceosome activation. Mutations in the N-terminal bromodomain-like region of Prp8 (U5 snRNP) suppress the cold-sensitive prp28-1 mutant at both the early CC2 assembly and later activation steps, placing Prp8 as a regulator of both ATP-independent and ATP-dependent Prp28 functions. Genetic suppressor screen in S. cerevisiae, in vivo and in vitro spliceosome assembly assays, commitment complex analysis RNA (New York, N.Y.) Medium 24231520
2021 Yeast Prp28 transiently interacts with the conserved 5' splice-site GU dinucleotide and makes splicing-dependent contacts with U1 snRNP protein U1C and tri-snRNP proteins Prp8, Brr2, and Snu114. Phosphorylated Npl3 (but not unphosphorylated Npl3) potentiates Prp28's ATPase activity, proposing Npl3 as a functional counterpart of the metazoan-specific phosphorylated N-terminal region of Prp28/DDX23. Co-immunoprecipitation, in vitro ATPase activity assay with phosphorylated vs. unphosphorylated Npl3, splicing-dependent crosslinking Nature communications Medium 34035302
2019 Human DDX23 binds low-molecular-weight poly(I:C) (dsRNA) through its N-terminal region. Upon poly(I:C) or VSV stimulation, DDX23 translocates from the nucleus to the cytoplasm and forms complexes with TRIF or MAVS to initiate downstream NF-κB and IRF3 signaling. Knockdown of DDX23 enhances VSV replication and reduces NF-κB/IRF3 activation. Poly(I:C) pull-down assay, Co-immunoprecipitation with TRIF and MAVS, siRNA knockdown, viral replication assay, immunofluorescence for subcellular localization Frontiers in immunology Medium 31620127
2020 DDX23 interacts with FMDV IRES domains III and IV and suppresses IRES-dependent translation. DDX23 also interacts with FMDV 3C proteinase, which degrades DDX23 via the lysosomal pathway. Overexpression of DDX23 reduces FMDV replication, while knockdown/knockout increases it. Pull-down assay, Co-immunoprecipitation, siRNA knockdown, CRISPR knockout, overexpression, IRES-driven reporter translation assay, confocal microscopy Viruses Medium 33255534
2021 DDX23 regulates mRNA processing of FOXM1 in ovarian cancer cells; DDX23 silencing reduces production of the FOXM1C oncogenic transcript and decreases FOXM1 protein. DDX23 transcription is directly activated by transcription factor E2F1, as shown by luciferase reporter and ChIP assays. Transcriptomic analysis of DDX23-silenced cells, ChIP assay, luciferase reporter assay, siRNA knockdown, rescue experiments Frontiers in oncology Medium 34966670
2023 METTL3 methyltransferase directly m6A-modifies DDX23 mRNA in a YTHDF1-dependent manner, enhancing DDX23 expression. Elevated DDX23 activates PI3K/Akt signaling; DDX23 silencing suppresses PI3K/Akt activation and reduces pancreatic cancer cell malignancy and gemcitabine resistance. MeRIP-qPCR for m6A site identification, siRNA knockdown, overexpression rescue experiments, Western blotting for PI3K/Akt pathway components Cell death & disease Low 36977668
2024 SRSF1 directly interacts with DDX23/PRP28; the interaction is mediated by the N-terminal RS-like domain of DDX23 and both RRM1 and the RS domain of SRSF1, as validated by bimolecular fluorescence complementation and in vitro binding assays. The RS-like region of DDX23's N-terminal domain is important for spliceosome incorporation, and larger N-terminal deletions alter DDX23's subnuclear localization. Proximity labeling (BioID) with mass spectrometry, bimolecular fluorescence complementation (BiFC), in vitro binding assays, deletion mutagenesis with subnuclear localization imaging Proceedings of the National Academy of Sciences of the United States of America High 38743621
2025 Polymerase κ (Pol κ) physically interacts with DDX23 and recruits DDX23 to R-loop loci in chromatin to promote DDX23-mediated R-loop resolution. Individual ablation of either Pol κ or DDX23 augments R-loop accumulation in cells. Proximity labeling (BioID) and affinity pull-down followed by LC-MS/MS, co-immunoprecipitation, R-loop immunofluorescence (S9.6 antibody), individual KO/KD of Pol κ and DDX23 Analytical chemistry Medium 41949541
2025 LncPEDS1-AS interacts with splicing factor DDX23 to form a nuclear RNA-protein complex that facilitates splicing and maturation of PEDS1 pre-mRNA, thereby promoting resistance to lipid peroxidation in UTUC. RNA immunoprecipitation, co-immunoprecipitation, ASO-mediated knockdown with functional ROS/lipid peroxidation assays Cell death & disease Low 41360761
2016 Crystal structure of Prp28 from thermophilic fungus Chaetomium thermophilum (ortholog of DDX23) determined at 3.2 Å resolution, confirming conservation of the two-RecA-domain open conformation seen in yeast and human Prp28 structures. X-ray crystallography at 3.2 Å resolution Acta crystallographica. Section F, Structural biology communications Medium 27139834

Source papers

Stage 0 corpus · 27 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2008 Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. Nature structural & molecular biology 114 18425142
2017 Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation. Cell reports 95 28076779
2016 A spliceosome intermediate with loosely associated tri-snRNP accumulates in the absence of Prp28 ATPase activity. Nature communications 66 27377154
2015 DEAD-box RNA helicase DDX23 modulates glioma malignancy via elevating miR-21 biogenesis. Brain : a journal of neurology 66 26121981
1994 PRP28, a 'DEAD-box' protein, is required for the first step of mRNA splicing in vitro. Nucleic acids research 66 7520570
2023 METTL3 enhances pancreatic ductal adenocarcinoma progression and gemcitabine resistance through modifying DDX23 mRNA N6 adenosine methylation. Cell death & disease 40 36977668
2019 DDX23, an Evolutionary Conserved dsRNA Sensor, Participates in Innate Antiviral Responses by Pairing With TRIF or MAVS. Frontiers in immunology 36 31620127
2008 The Caenorhabditis elegans DDX-23, a homolog of yeast splicing factor PRP28, is required for the sperm-oocyte switch and differentiation of various cell types. Developmental dynamics : an official publication of the American Association of Anatomists 31 18729217
2014 Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28. Nucleic acids research 22 25303995
2014 Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28. Acta crystallographica. Section D, Biological crystallography 21 24914973
2020 The DDX23 Negatively Regulates Translation and Replication of Foot-and-Mouth Disease Virus and Is Degraded by 3C Proteinase. Viruses 20 33255534
2014 Structure-function analysis of the Yhc1 subunit of yeast U1 snRNP and genetic interactions of Yhc1 with Mud2, Nam8, Mud1, Tgs1, U1 snRNA, SmD3 and Prp28. Nucleic acids research 20 24497193
2021 Syndromic neurodevelopmental disorder associated with de novo variants in DDX23. American journal of medical genetics. Part A 19 34050707
2015 A novel function for the DEAD-box RNA helicase DDX-23 in primary microRNA processing in Caenorhabditis elegans. Developmental biology 19 26601717
2017 DDX23-Linc00630-HDAC1 axis activates the Notch pathway to promote metastasis. Oncotarget 18 28473661
2013 An unanticipated early function of DEAD-box ATPase Prp28 during commitment to splicing is modulated by U5 snRNP protein Prp8. RNA (New York, N.Y.) 17 24231520
2021 Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling. Nature communications 12 34035302
2021 Splicing Factor DDX23, Transcriptionally Activated by E2F1, Promotes Ovarian Cancer Progression by Regulating FOXM1. Frontiers in oncology 10 34966670
2024 SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proceedings of the National Academy of Sciences of the United States of America 8 38743621
2024 DEAD-box RNA helicase DDX-23 mediates dietary restriction induced health span in Caenorhabditis elegans. GeroScience 8 39578298
2019 4-Amino-2-trifluoromethyl-phenyl retinate induced differentiation of human myelodysplastic syndromes SKM-1 cell lines by up-regulating DDX23. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 6 31855738
2016 Structural analysis of the spliceosomal RNA helicase Prp28 from the thermophilic eukaryote Chaetomium thermophilum. Acta crystallographica. Section F, Structural biology communications 5 27139834
2023 DDX23 of black carp negatively regulates MAVS-mediated antiviral signaling in innate immune activation. Developmental and comparative immunology 1 37164277
2026 Polymerase κ Recruits DDX23 To Promote R-Loop Resolution. Analytical chemistry 0 41949541
2025 3A and 2B proteins of SVA play chess game with host restriction factor DDX23 by apoptotic pathway. Journal of virology 0 40956085
2025 Structural Characterization of DDX23 5' UTR Regulatory Elements and Their Targeting by LNA-Modified Antisense Oligonucleotides. International journal of molecular sciences 0 41303530
2025 LncPEDS1-AS promotes UTUC resistance to lipid peroxidation by regulating PEDS1 expression via DDX23. Cell death & disease 0 41360761

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