Affinage

DBF4

Protein DBF4 homolog A · UniProt Q9UBU7

Length
674 aa
Mass
76.9 kDa
Annotated
2026-04-28
100 papers in source corpus 35 papers cited in narrative 35 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

DBF4 is the essential regulatory subunit of the Dbf4-dependent kinase (DDK), whose primary function is to trigger eukaryotic DNA replication initiation by phosphorylating MCM helicase subunits at licensed origins. Crystal and cryo-EM structures show that DBF4 wraps around CDC7 in a bipartite interface—its motif C stabilizes the CDC7 αC helix to activate kinase activity, its HBRCT domain anchors DDK onto the MCM double hexamer via Mcm2, and an autoinhibitory loop occupying the CDC7 active site is displaced upon substrate engagement, enabling phosphorylation of the Mcm4 N-terminal serine/threonine-rich domain (NSD), Mcm2, and Mcm6; these phosphorylations recruit Sld3 and Cdc45 to assemble the replicative CMG helicase (PMID:23064647, PMID:34963704, PMID:35614055, PMID:26912723, PMID:20054399). DBF4 protein levels oscillate through APC-dependent degradation in G1, and during replication stress, the checkpoint kinase Rad53 directly phosphorylates DBF4 via a non-canonical FHA1 interaction, blocking DDK docking onto double hexamers and suppressing late-origin firing (PMID:10805723, PMID:20835227, PMID:22130670, PMID:27681475, PMID:34963704). Beyond S-phase control, DDK phosphorylates Mer2 (with CDK) and Sum1 to promote meiotic DSB formation and NDT80 transcription, activates Mus81-Mms4 nuclease in mitosis together with Cdc5, and in Drosophila the DBF4 ortholog Chiffon forms the CHAT histone acetyltransferase complex with Gcn5, an essential Cdc7-independent function (PMID:18245450, PMID:22106412, PMID:28096179, PMID:30559249).

Mechanistic history

Synthesis pass · year-by-year structured walk · 17 steps
  1. 1989 Medium

    The first indication that DBF4 operates at the G1/S boundary came from showing its transcript is cell-cycle regulated with a late-G1 peak, coinciding with DNA synthesis genes.

    Evidence Northern blotting and cell-cycle arrest/release in yeast

    PMID:2644125

    Open questions at the time
    • Protein-level regulation not addressed
    • No mechanistic link to DNA replication machinery
  2. 1992 High

    Allele-specific genetic suppression between DBF4 and CDC7 established that Dbf4 and Cdc7 function as a physically linked kinase unit required for replication initiation.

    Evidence Multicopy suppression genetics in S. cerevisiae temperature-sensitive mutants

    PMID:1592236

    Open questions at the time
    • Physical interaction not directly demonstrated
    • Kinase activity not measured
  3. 1994 High

    Dbf4 was shown to interact with replication origins in vivo and to positively regulate Cdc7 kinase activity, establishing the model that Dbf4 recruits active Cdc7 to origins.

    Evidence Two-hybrid and one-hybrid screens, in vivo origin interaction assay in yeast

    PMID:8066465

    Open questions at the time
    • Origin-interaction specificity mechanism unknown
    • Substrate identity unresolved
  4. 1997 High

    Identification of MCM2 as a direct DDK substrate, combined with genetic suppression of mcm2-1 by a dbf4 allele, established that DDK phosphorylates the MCM helicase to trigger replication, while parallel work placed DDK and CDC45 in an interdependent pathway at origins.

    Evidence Co-immunoprecipitation, in vitro kinase assay, genetic suppressor screen; genetic epistasis with CDC45

    PMID:9356482 PMID:9407029

    Open questions at the time
    • Specific MCM phosphosites not mapped
    • Functional consequence of MCM phosphorylation unknown
  5. 2000 High

    DDK activity was shown to be cell-cycle regulated through APC-dependent Dbf4 degradation in G1, and DDK was placed downstream of S-CDK activation, ordering the two kinase pathways in replication initiation.

    Evidence Protein stability assays, cell-cycle synchronization, genetic ordering, in vitro kinase assay in yeast

    PMID:10805723

    Open questions at the time
    • Mechanism of APC recognition of Dbf4 not detailed
    • Relationship between DDK and CDK at the substrate level unclear
  6. 2006 High

    Phosphosite mapping and functional rescue experiments in human cells demonstrated that Cdc7-Dbf4 phosphorylates MCM2 on chromatin to stimulate MCM2-7 ATPase activity, providing the first mechanistic consequence of DDK phosphorylation for helicase activation; concurrent work revealed DDK also phosphorylates CAF1 p150 to coordinate chromatin assembly with replication.

    Evidence siRNA rescue with phosphomimetic MCM2, in vitro ATPase assay, mass spectrometry; co-IP and kinase assay for CAF1 in human cells

    PMID:16826239 PMID:16899510

    Open questions at the time
    • MCM4 and MCM6 phosphorylation by DDK not yet characterized
    • In vivo relevance of CAF1 phosphorylation not fully tested
  7. 2008 High

    Multiple studies converged to show DDK has critical functions beyond replication: DDK phosphorylates Mer2 (primed by CDK) to initiate meiotic DSBs and recruits the monopolin complex for meiosis I kinetochore monoorientation, while in metazoans DDK attenuates ATR-Chk1 checkpoint signaling rather than being inhibited by it.

    Evidence In vitro kinase assays, phosphomimetic rescue, meiotic DSB assays, genetic analysis in yeast; Xenopus extract reconstitution and HeLa overexpression for checkpoint attenuation

    PMID:18245450 PMID:19013276 PMID:19111665

    Open questions at the time
    • How DDK attenuates checkpoint in molecular terms unclear
    • Monopolin recruitment mechanism (Lrs4 phosphorylation) not fully validated
  8. 2009 High

    Biochemical reconstitution showed Dbf4 alone binds Mcm2 tightly and recruits Cdc7, and that DDK specifically targets origin-loaded MCM conformations, explaining spatial restriction of firing; meanwhile, LEDGF was found to stimulate Cdc7-DBF4 activity by relieving an autoinhibition encoded in the DBF4 C-terminus.

    Evidence In vitro pre-RC reconstitution, DDK binding/phosphorylation assays; co-IP and kinase assay with DBF4 truncations

    PMID:19270162 PMID:19692334 PMID:19864417

    Open questions at the time
    • Structural basis of origin-loaded MCM selectivity unknown
    • LEDGF relevance in vivo not confirmed
  9. 2010 High

    Genetic experiments in yeast demonstrated that the sole essential DDK function is to relieve the inhibitory activity of the Mcm4 NSD, while Rad53 was shown to inhibit DDK directly by phosphorylating Dbf4, acting redundantly with Sld3 phosphorylation to block late-origin firing during replication stress.

    Evidence mcm4 NSD deletion bypass genetics; in vitro Rad53-Dbf4 phosphorylation and origin-firing assays

    PMID:20054399 PMID:20835227

    Open questions at the time
    • Structural mechanism of NSD relief not visualized
    • Whether Rad53 phosphorylation of Dbf4 blocks DDK-DH binding not yet tested
  10. 2010 High

    Domain dissection of Dbf4 revealed that motif C encodes a zinc finger required for origin DNA association and Mcm2 binding but not for Cdc7 interaction, and that Dbf4 also binds the Cdc5 polo-box domain through a non-canonical interface to regulate late-origin firing.

    Evidence Mutagenesis, ChIP, two-hybrid, kinase assay, binding assays in yeast

    PMID:20436286 PMID:21036905

    Open questions at the time
    • Whether Dbf4-Cdc5 interaction is direct at endogenous levels unclear
    • Structural basis of motif C zinc finger-origin interaction not resolved
  11. 2011 High

    Crystal structure of the Dbf4 BRCT domain revealed a unique N-terminal helix essential for Rad53 interaction and checkpoint function, while DDK was also shown to regulate meiotic transcription by phosphorylating Sum1 to derepress NDT80.

    Evidence Crystal structure, mutagenesis, binding assays; mass spectrometry phosphosite mapping and meiotic transcription assays

    PMID:22106412 PMID:22130670

    Open questions at the time
    • Whether Sum1 phosphorylation by DDK is cell-cycle regulated unknown
    • BRCT helix contribution to DDK-DH docking not tested
  12. 2012 High

    The first crystal structures of the human CDC7–DBF4 complex revealed the bipartite wrapping architecture: DBF4 motif C contacts the CDC7 N-lobe to stabilize αC helix positioning and activate kinase activity, while motif M tethers to the C-lobe.

    Evidence X-ray crystallography of human CDC7–DBF4 with nucleotide/inhibitor ligands

    PMID:23064647

    Open questions at the time
    • Structure captured without substrate; MCM-bound state not resolved
    • DBF4 autoinhibitory loop not visualized
  13. 2013 High

    Structural and biochemical studies established that Rad53 FHA1 uses a non-canonical, phosphorylation-independent surface to bind Dbf4 while simultaneously recognizing Cdc7 phosphopeptide through its canonical site, functioning as an 'AND' logic gate for specificity of DDK inhibition during checkpoint activation.

    Evidence Crystal structures, NMR, mutagenesis, biochemical binding, genotoxic stress assays

    PMID:23564203 PMID:24285546 PMID:27681475

    Open questions at the time
    • Whether the dual-recognition logic operates in metazoans unknown
    • Stoichiometry of Rad53-DDK complex in vivo unclear
  14. 2016 High

    Reconstitution experiments identified Sld3 as the essential 'reader' of DDK-dependent MCM phosphorylation: Sld3 specifically binds DDK-phosphorylated Mcm4 and Mcm6 peptides and recruits Cdc45, closing the DDK→phospho-MCM→Sld3→Cdc45 pathway for CMG helicase assembly.

    Evidence Reconstituted replication system, phosphopeptide binding, phosphomimetic bypass of DDK

    PMID:26912723

    Open questions at the time
    • Structural basis of Sld3 phosphopeptide recognition not determined
    • Whether additional readers exist not excluded
  15. 2017 High

    DDK was shown to phosphorylate Mus81-Mms4 in collaboration with Cdc5, with Rtt107 acting as a scaffold, establishing that DDK activates structure-selective nuclease activity in mitosis for joint molecule resolution.

    Evidence Co-IP, in vitro kinase assay, Mus81 nuclease activity assay, genetic analysis in yeast

    PMID:28096179

    Open questions at the time
    • Specific DDK phosphosites on Mms4 not mapped
    • Whether this function is conserved in human cells unknown
  16. 2019 High

    The Drosophila DBF4 ortholog Chiffon was found to form the CHAT histone acetyltransferase complex with Gcn5/Ada2a/Ada3/Sgf29, a function essential for viability and separable from its Cdc7-activating role, revealing a Cdc7-independent essential function for DBF4 in metazoans.

    Evidence Co-IP/mass spectrometry, genetic domain dissection, histone acetylation assays in Drosophila

    PMID:30559249

    Open questions at the time
    • Whether mammalian DBF4 participates in an analogous HAT complex is unknown
    • CHAT complex substrates beyond bulk histones not identified
  17. 2022 High

    Multiple cryo-EM structures of yeast DDK bound to MCM double hexamers revealed the complete docking mechanism: the Dbf4 HBRCT domain anchors DDK to Mcm2, while Dbf4 straddles the hexamer interface contacting Mcm4, Mcm6, and displacing the Mcm4 NSD for phosphorylation; the Dbf4 autoinhibitory loop occupies the Cdc7 active site and is released upon substrate engagement; Rad53 phosphorylation of Dbf4 blocks DH docking and active-site access.

    Evidence Cryo-EM structure determination (multiple independent studies), biochemical truncation and mutagenesis, in vitro kinase assays

    PMID:34963704 PMID:35296675 PMID:35614055

    Open questions at the time
    • How Dbf4 autoinhibitory loop release is triggered at the atomic level remains unclear
    • Structures of DDK bound to post-fired MCM states not available
    • Conformational transitions during sequential phosphorylation of Mcm4, Mcm2, Mcm6 not resolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include: whether the CHAT histone acetyltransferase function of DBF4 is conserved in mammals; the structural basis for DDK substrate switching between replication, meiotic, and mitotic targets; and whether DDK has additional kinase-independent scaffolding roles at replication forks beyond origin firing.
  • Mammalian CHAT complex conservation not tested
  • No structural model of DDK engaged with meiotic substrates (Mer2, Sum1)
  • Post-initiation roles of DDK at elongating forks remain poorly defined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 9 GO:0140096 catalytic activity, acting on a protein 6 GO:0060090 molecular adaptor activity 5
Localization
GO:0005694 chromosome 6 GO:0005634 nucleus 2
Pathway
R-HSA-69306 DNA Replication 11 R-HSA-73894 DNA Repair 6 R-HSA-1640170 Cell Cycle 4 R-HSA-1474165 Reproduction 3 R-HSA-4839726 Chromatin organization 2
Partners
CDC5CDC7LEDGFMCM2MER2MUS81RAD53SLD3
Complex memberships
CHAT (Chiffon Histone Acetyltransferase)DDK (Dbf4-Cdc7 kinase)

Evidence

Reading pass · 35 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1992 DBF4 encodes the regulatory subunit of the Cdc7 protein kinase; multicopy DBF4 suppresses temperature-sensitive cdc7 mutations in an allele-specific manner, and conversely, multicopy CDC7 suppresses dbf4 mutations, indicating direct or indirect physical interaction between Cdc7 and Dbf4 for DNA replication initiation at the G1/S transition. Genetic suppression analysis, multicopy suppression, allele-specificity tests Genetics High 1592236
1989 DBF4 transcript is cell cycle-regulated, peaking in late G1 phase coincident with genes involved in DNA synthesis, consistent with a role in S phase entry. Northern blotting, cell cycle arrest/release experiments Experimental cell research Medium 2644125
1994 Dbf4 protein interacts with yeast replication origins in vivo and positively regulates Cdc7 kinase activity; a model is proposed in which Dbf4 recruits Cdc7 to initiation complexes at origins. Two-hybrid and one-hybrid screens, in vivo origin interaction assay Science High 8066465
1997 Cdc7-Dbf4 physically interacts with Mcm2 and phosphorylates Mcm2 and three other Mcm2-7 family members in vitro; genetic suppression of mcm2-1 by a dbf4 allele establishes that Dbf4 regulates Mcm2 function for DNA replication initiation. Genetic suppressor screen, co-immunoprecipitation, in vitro kinase assay, in vivo phosphorylation analysis Genes & development High 9407029
1997 CDC45 and CDC7/DBF4 are functionally interdependent for triggering replication initiation at origins in late G1, after pre-RC assembly. Genetic epistasis, cell cycle synchronization, loss-of-function analysis Proceedings of the National Academy of Sciences of the United States of America Medium 9356482
1999 Rad53 kinase positively regulates Dbf4 by binding to it (two-hybrid interaction) and maintaining steady-state DBF4 mRNA and protein levels; this establishes that RAD53 promotes DNA replication initiation through DBF4, separable from its checkpoint function. Two-hybrid analysis, mRNA/protein quantification in rad53 mutants Genetics Medium 10049915
2000 DDK (Cdc7-Dbf4) activity is cell cycle regulated through Dbf4 protein instability; Dbf4 is degraded by the APC during G1. DDK can execute its replication function only after S-CDK activation; Cdc45, which binds chromatin only after S-CDK activation, is phosphorylated by DDK in vitro, suggesting it is a critical downstream substrate linking the two kinase pathways. Protein stability assays, cell cycle synchronization, genetic ordering, in vitro kinase assay Molecular and cellular biology High 10805723
2006 Human Cdc7/Dbf4 phosphorylates MCM2 on specific residues during G1/S on chromatin; phosphomimetic MCM2 restores DNA replication in siRNA-depleted cells whereas non-phosphorylatable MCM2 does not; phosphorylation of MCM2 by Cdc7/Dbf4 increases the ATPase activity of the MCM2-7 complex in vitro. Immunoblotting, immunofluorescence, siRNA rescue, in vitro ATPase assay, mass spectrometry phosphosite identification Molecular biology of the cell High 16899510
2006 Cdc7-Dbf4 directly phosphorylates the p150 (large) subunit of chromatin assembly factor 1 (CAF1); this phosphorylation changes p150 oligomerization state and promotes its binding to PCNA, coordinating chromatin assembly with DNA replication. A Cdc7-Dbf4/CAF1-p150 complex exists specifically in S phase. Co-immunoprecipitation, in vitro kinase assay, PCNA binding assay, Cdc7-depleted extract functional assay EMBO reports High 16826239
2007 Dbf4 is a substrate of Chk1 kinase in vitro and interacts with Chk1 in vivo; overexpression of Dbf4 abrogates the S-phase checkpoint response to UVC but not ionizing radiation, implicating Dbf4-dependent kinase as a target of the ATR/Chk1-dependent S-checkpoint. In vitro kinase assay, co-immunoprecipitation, FLAG-tag overexpression, checkpoint assay The Journal of biological chemistry Medium 17276990
2008 In S. cerevisiae, DDK (Cdc7-Dbf4) promotes double-strand break formation in meiosis and recruits the monopolin complex to kinetochores (likely via phosphorylation of Lrs4), together with polo-kinase Cdc5/Spo13, to establish monopolar kinetochore attachment required for reductional chromosome segregation at meiosis I. Genetic analysis, meiotic phenotyping, mass spectrometry, kinase assay, co-immunoprecipitation Cell High 19013276
2008 In S. pombe (ortholog), the Cdc7-Dbf4 kinase (Hsk1-Dfp1/Him1) is required for full Rad53 activation during replication stress; recombinant Cdc7-Dbf4 phosphorylates Rad53 in vitro, suggesting a positive regulatory role in the replication checkpoint. In vitro kinase assay, checkpoint assay in cdc7-deleted cells, Rad53 phosphorylation analysis Gene Medium 18372119
2008 DDK (Cdc7-Dbf4) and CDK-S (Cdc28-Clb5) collaboratively phosphorylate Mer2 to initiate meiotic recombination: CDK-S phosphorylates Mer2 Ser30, which primes subsequent DDK phosphorylation of Ser29, creating a negatively charged patch necessary for double-strand break formation. In vitro kinase assays, phosphomimetic mutant analysis, meiotic DSB assay Genes & development High 18245450
2008 Complex formation, chromatin association, and kinase activity of Ddk (Cdc7-Dbf4/Drf1) are not inhibited during the DNA-damage S-phase checkpoint in Xenopus egg extracts and mammalian cells; instead, Ddk downregulates ATR-Chk1 checkpoint signaling when added to extracts or overexpressed, indicating Ddk acts as an upstream attenuator of checkpoint signaling. Xenopus cell-free extract reconstitution, HeLa cell overexpression, kinase activity assays, checkpoint signaling readouts Molecular cell High 19111665
2009 Dbf4 forms a heterodimer with Cdc7 that phosphorylates Mcm2 with substantially higher specific activity than Cdc7 alone; Dbf4 alone binds Mcm2 tightly and recruits Cdc7 to phosphorylate it. DDK phosphorylates Mcm2 at Ser-164 and Ser-170; phosphorylation of Ser-170 is required for cell growth and bypassed by mcm5-bob1. In vitro kinase assay, binding assay, phosphosite mutagenesis, yeast genetic rescue The Journal of biological chemistry High 19692334
2009 Incorporation of Mcm2-7 into the pre-RC on origin DNA changes the specificity of DDK phosphorylation; DDK targets a conformationally distinct subpopulation of origin-linked Mcm2-7 via tight Dbf4-dependent association, ensuring spatially and temporally restricted DDK action. In vitro pre-RC reconstitution, DDK binding and phosphorylation assays, chromatin fractionation Genes & development High 19270162
2009 LEDGF interacts with Cdc7-ASK (DBF4 in human); both kinase subunits co-immunoprecipitate with endogenous LEDGF; LEDGF stimulates Cdc7-ASK enzymatic activity >10-fold in vitro by relieving autoinhibition imposed by the C-terminus of ASK/DBF4; the interaction requires autophosphorylation of the kinase and the C-terminal 50 residues of ASK/DBF4. Co-immunoprecipitation, in vitro kinase assay, truncation analysis, phosphorylation site mapping The Journal of biological chemistry High 19864417
2010 The N-terminal serine/threonine-rich domain (NSD) of Mcm4 contains an inhibitory activity; the sole essential function of DDK (Dbf4-Cdc7) is to relieve this inhibitory activity. Combined mcm4 NSD deletion with CDK bypass mutations enables DNA synthesis in G1 when DDK is limited, but DDK is still required for efficient S-phase progression and intra-S checkpoint activation. Yeast genetic analysis, mcm4 NSD deletion, CDK bypass mutations, S-phase progression assays Nature High 20054399
2010 The S. cerevisiae checkpoint kinase Rad53 inhibits DDK by directly phosphorylating Dbf4, and inhibits CDK pathway by phosphorylating Sld3, acting redundantly to block late origin firing during the intra-S-phase checkpoint. In vitro kinase assays, origin firing assays, genetic epistasis, phosphorylation site mapping Nature High 20835227
2010 Dbf4 inhibits Cdc5 (polo-like kinase) function through direct binding to the Cdc5 polo-box domain (PBD) via a non-canonical, non-phosphodependent interface; mutation of the PBD-Dbf4 binding site allows late-origin firing and affects mitotic exit network regulation. Biochemical binding assays, yeast genetic analysis, mutagenesis of Dbf4 PBD-binding residues The Journal of biological chemistry Medium 21036905
2010 Dbf4 motif C encodes a zinc finger required for association with ARS1 origin DNA and Mcm2 (but not Cdc7, Rad53, or Orc2); motif C mutations impair Mcm2 phosphorylation and compromise S-phase entry and progression, as well as resistance to prolonged genotoxic stress. Mutagenesis, yeast two-hybrid, ChIP at ARS1, in vitro kinase assay, cell cycle analysis Cell cycle High 20436286
2011 Saccharomyces cerevisiae Dbf4 contains a BRCT domain with a unique N-terminal helix required for interaction with the checkpoint kinase Rad53; mutations destabilizing this helix abolish the Dbf4-Rad53 interaction and disrupt checkpoint function. Crystal structure determination, mutagenesis, binding assays The Journal of biological chemistry High 22130670
2011 Cdc7-Dbf4 acts as a gene-specific regulator of meiotic transcription by promoting NDT80 transcription through Cdc7-dependent phosphorylation of Sum1 (11 meiosis-specific sites identified by mass spectrometry), thereby relieving Sum1-Rfm1-Hst1 repression of NDT80. Mass spectrometry phosphosite mapping, genetic analysis, meiotic transcription assays Molecular and cellular biology Medium 22106412
2012 Crystal structures of human CDC7-DBF4 complex reveal that DBF4 wraps around CDC7, burying ~6,000 Ų in a bipartite interface; DBF4 motif C (effector domain) is essential and sufficient to activate CDC7 by binding its N-terminal lobe and stabilizing the αC helix; DBF4 motif M tethers onto the CDC7 C-terminal lobe. X-ray crystallography of human CDC7-DBF4 with nucleotide and inhibitor ligands, structure-function analysis Nature structural & molecular biology High 23064647
2013 The Rad53 FHA1 domain interacts with Dbf4 through a non-canonical, phosphorylation-independent interface distinct from the canonical phosphoepitope-binding site; this interaction is critical for Rad53 to phosphorylate Dbf4 and suppress late origin firing during replication stress. Abrogation of the Rad53-Dbf4 physical interaction prevents Dbf4 phosphorylation and allows late-origin firing. Biochemical binding assays, mutagenesis, yeast genetic analysis, genotoxic stress sensitivity Genetics High 23564203
2013 The non-canonical FHA1-Dbf4 interface involves a novel surface on Rad53 FHA1 domain not conserved in FHA2; NMR and biochemical analysis establish the molecular basis for phosphorylation-independent Rad53-Dbf4 recognition; mutations within this surface cause hypersensitivity to genotoxic stress. NMR, biochemical binding assays, mutagenesis, genotoxic stress assays The Journal of biological chemistry High 24285546
2016 Sld3 is an essential 'reader' of DDK phosphorylation: it is recruited to the inactive MCM double hexamer in a DDK-dependent manner, binds specifically to DDK-phosphorylated peptides from Mcm4 and Mcm6, and then recruits Cdc45. Phosphomimicking Mcm4 and Mcm6 mutants bypass DDK requirement for replication, establishing DDK→phospho-MCM→Sld3 as the essential step. Reconstituted replication system, phosphopeptide binding assays, MCM and Sld3 mutant analysis, DDK-independent replication The EMBO journal High 26912723
2016 Crystal structures of Rad53 FHA1 bound to Dbf4 show that FHA1 uses a canonical interface for Cdc7 phosphopeptide recognition and a non-canonical interface for Dbf4 binding simultaneously, functioning as an 'AND' logic gate to enhance specificity of DDK inhibition. X-ray crystallography, biochemical binding assays Scientific reports High 27681475
2017 DDK (Cdc7-Dbf4) phosphorylates Mus81-Mms4 in conjunction with Cdc5 kinase; these two kinases bind and phosphorylate Mus81-Mms4 in an interdependent manner; DDK-mediated phosphorylation of Mms4 is strictly required for Mus81 nuclease activation in mitosis. The scaffold protein Rtt107 bridges DDK and Cdc5 to the Mus81-Mms4 complex. Genetic analysis, co-immunoprecipitation, in vitro kinase assay, Mus81 activity assay The EMBO journal High 28096179
2019 In Drosophila, Chiffon (DBF4 ortholog) forms the Chiffon Histone Acetyltransferase (CHAT) complex with Gcn5, Ada2a, Ada3, and Sgf29, distinct from its Cdc7-activating role. The CHAT-binding domain of Chiffon is essential for viability and histone acetylation, while the Cdc7-binding domain is not required for viability, establishing a Cdc7-independent essential function for DBF4/Chiffon. Co-IP/mass spectrometry, genetic analysis, histone acetylation assay, viability assays, dicistronic gene analysis Journal of cell science High 30559249
2021 Cryo-EM structure of S. cerevisiae DDK bound to the MCM double hexamer (DH) reveals that DDK docks onto one MCM ring via the Dbf4 docking domain and phosphorylates the opposed ring; truncation of the Dbf4 docking domain abrogates DH phosphorylation without affecting Cdc7 kinase activity; Rad53 phosphorylation of Dbf4 impairs DH phosphorylation by blocking DDK binding to DHs and interfering with the Cdc7 active site. Cryo-EM structure determination, biochemical truncation and mutagenesis, in vitro kinase assay Nature structural & molecular biology High 34963704
2022 Cryo-EM and biochemical analysis reveal that Dbf4 HBRCT domain anchors DDK to Mcm2, enabling DDK to straddle the MCM double-hexamer interface; a rotation of DDK along this anchoring point allows phosphorylation of Mcm2, Mcm4 and Mcm6; the Dbf4 inhibitory loop occupies the Cdc7 active site and is disengaged upon conformational changes. Cryo-EM structure determination, biochemical interaction analysis Nature communications High 35614055
2022 Cryo-EM structures of yeast DDK bound to the MCM-DH show Dbf4 straddling the hexamer interface via Mcm2, Mcm6, and Mcm4 N-terminal domains; Dbf4 brings Cdc7 close to the Mcm4 NSD and displaces the NSD from its binding site on Mcm4-NTD, directly facilitating Cdc7 phosphorylation of this substrate; a Dbf4 inhibitory loop occupies the Cdc7 active center and is released upon kinase conformational changes. Cryo-EM structure determination, biochemical analysis Nature communications High 35296675
2005 XDbf4 (Xenopus DBF4 ortholog) is an inhibitor of the canonical Wnt signaling pathway required for early cardiac development; this function is independent of Cdc7 kinase regulation and operates through physical and functional interaction with Frodo, a Wnt signaling regulator. Gain- and loss-of-function experiments in Xenopus embryos, co-immunoprecipitation with Frodo, cardiac marker assays Developmental cell Medium 15866161
2008 A strong origin of replication is located at the human DBF4 promoter locus; the locus contains two initiation zones with two ORC binding sites. Replication initiates at zone I and proceeds toward zone II in an asymmetric bidirectional mode. Replication origin mapping (nascent strand abundance assay), ORC binding, DNase I hypersensitivity Nature structural & molecular biology Medium 18536724

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1998 Mammalian thioredoxin is a direct inhibitor of apoptosis signal-regulating kinase (ASK) 1. The EMBO journal 2039 9564042
2010 Everything you wanted to know about Markov State Models but were afraid to ask. Methods (San Diego, Calif.) 504 20570730
1990 Cryopreservation of mammalian sperm: what we ask them to survive. Journal of andrology 384 2179184
1997 Mcm2 is a target of regulation by Cdc7-Dbf4 during the initiation of DNA synthesis. Genes & development 259 9407029
2010 The Dbf4-Cdc7 kinase promotes S phase by alleviating an inhibitory activity in Mcm4. Nature 248 20054399
2010 Checkpoint-dependent inhibition of DNA replication initiation by Sld3 and Dbf4 phosphorylation. Nature 225 20835227
1994 Interaction of Dbf4, the Cdc7 protein kinase regulatory subunit, with yeast replication origins in vivo. Science (New York, N.Y.) 179 8066465
2009 The roles of ASK family proteins in stress responses and diseases. Cell communication and signaling : CCS 174 19389260
2008 Dbf4-dependent CDC7 kinase links DNA replication to the segregation of homologous chromosomes in meiosis I. Cell 150 19013276
2001 CHIF, a member of the FXYD protein family, is a regulator of Na,K-ATPase distinct from the gamma-subunit. The EMBO journal 122 11483503
2008 Cdc28-Clb5 (CDK-S) and Cdc7-Dbf4 (DDK) collaborate to initiate meiotic recombination in yeast. Genes & development 113 18245450
2019 Everything You Always Wanted to Know about β3-AR * (* But Were Afraid to Ask). Cells 112 30995798
2006 Essential role of phosphorylation of MCM2 by Cdc7/Dbf4 in the initiation of DNA replication in mammalian cells. Molecular biology of the cell 110 16899510
2016 Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation. The EMBO journal 108 26912723
2009 Incorporation into the prereplicative complex activates the Mcm2-7 helicase for Cdc7-Dbf4 phosphorylation. Genes & development 107 19270162
2022 DKK3 ameliorates neuropathic pain via inhibiting ASK-1/JNK/p-38-mediated microglia polarization and neuroinflammation. Journal of neuroinflammation 103 35658977
2016 Everything we always wanted to know about furosemide but were afraid to ask. American journal of physiology. Renal physiology 100 26911852
2000 Hierarchy of S-phase-promoting factors: yeast Dbf4-Cdc7 kinase requires prior S-phase cyclin-dependent kinase activation. Molecular and cellular biology 100 10805723
2020 Distribution and Antifungal Susceptibility of Candida Species Causing Candidemia in China: An Update From the CHIF-NET Study. The Journal of infectious diseases 95 32176789
2012 In vitro susceptibilities of yeast species to fluconazole and voriconazole as determined by the 2010 National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) study. Journal of clinical microbiology 91 23035204
1992 Temperature-sensitive cdc7 mutations of Saccharomyces cerevisiae are suppressed by the DBF4 gene, which is required for the G1/S cell cycle transition. Genetics 91 1592236
1997 CDC45 is required in conjunction with CDC7/DBF4 to trigger the initiation of DNA replication. Proceedings of the National Academy of Sciences of the United States of America 86 9356482
2018 Five-Year National Surveillance of Invasive Candidiasis: Species Distribution and Azole Susceptibility from the China Hospital Invasive Fungal Surveillance Net (CHIF-NET) Study. Journal of clinical microbiology 80 29743305
2008 Everything you wanted to know about small RNA but were afraid to ask. Laboratory investigation; a journal of technical methods and pathology 78 18427554
1989 The yeast gene, DBF4, essential for entry into S phase is cell cycle regulated. Experimental cell research 77 2644125
2002 A functional interaction between CHIF and Na-K-ATPase: implication for regulation by FXYD proteins. American journal of physiology. Renal physiology 74 12217851
2019 Ginsenoside Re Inhibits ROS/ASK-1 Dependent Mitochondrial Apoptosis Pathway and Activation of Nrf2-Antioxidant Response in Beta-Amyloid-Challenged SH-SY5Y Cells. Molecules (Basel, Switzerland) 70 31344860
1996 Cellular localization and regulation of CHIF in kidney and colon. The American journal of physiology 70 8843704
2012 A comprehensive analysis of interaction and localization of Arabidopsis SKP1-like (ASK) and F-box (FBX) proteins. PloS one 69 23166809
2004 Identification of ASK and clock-associated proteins as molecular partners of LKP2 (LOV kelch protein 2) in Arabidopsis. Journal of experimental botany 69 15310821
2000 The Cdc7/Dbf4 protein kinase: target of the S phase checkpoint? EMBO reports 68 11269496
2000 The modes of action of juvenile hormones: some questions we ought to ask. Insect biochemistry and molecular biology 66 10876109
2017 The regulatory and signaling mechanisms of the ASK family. Advances in biological regulation 63 28669716
2012 Crystal structure of human CDC7 kinase in complex with its activator DBF4. Nature structural & molecular biology 61 23064647
2006 The replication kinase Cdc7-Dbf4 promotes the interaction of the p150 subunit of chromatin assembly factor 1 with proliferating cell nuclear antigen. EMBO reports 58 16826239
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