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5Y27

Crystal structure of Se-Met Dpb4-Dpb3

Summary for 5Y27
Entry DOI10.2210/pdb5y27/pdb
DescriptorDNA polymerase epsilon subunit D, Putative transcription factor C16C4.22, GLYCEROL, ... (4 entities in total)
Functional Keywordsheterodimer, histone fold complex, dna binging, epigenetic, dna binding protein
Biological sourceSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
More
Cellular locationNucleus : P87174 C6Y4D0
Total number of polymer chains2
Total formula weight38185.61
Authors
Li, Y.,Gao, F.,Su, M.,Zhang, F.B.,Chen, Y.H. (deposition date: 2017-07-24, release date: 2018-01-24, Last modification date: 2024-11-06)
Primary citationHe, H.,Li, Y.,Dong, Q.,Chang, A.Y.,Gao, F.,Chi, Z.,Su, M.,Zhang, F.,Ban, H.,Martienssen, R.,Chen, Y.H.,Li, F.
Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex.
Proc. Natl. Acad. Sci. U.S.A., 114:12524-12529, 2017
Cited by
PubMed Abstract: During DNA replication, chromatin is disrupted ahead of the replication fork, and epigenetic information must be restored behind the fork. How epigenetic marks are inherited through DNA replication remains poorly understood. Histone H3 lysine 9 (H3K9) methylation and histone hypoacetylation are conserved hallmarks of heterochromatin. We previously showed that the inheritance of H3K9 methylation during DNA replication depends on the catalytic subunit of DNA polymerase epsilon, Cdc20. Here we show that the histone-fold subunit of Pol epsilon, Dpb4, interacts an uncharacterized small histone-fold protein, SPCC16C4.22, to form a heterodimer in fission yeast. We demonstrate that SPCC16C4.22 is nonessential for viability and corresponds to the true ortholog of Dpb3. We further show that the Dpb3-Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation in heterochromatin. We solve the 1.9-Å crystal structure of Dpb3-Dpb4 and reveal that they form the H2A-H2B-like dimer. Disruption of Dpb3-Dpb4 dimerization results in loss of heterochromatin silencing. Our findings reveal a link between histone deacetylation and H3K9 methylation and suggest a mechanism for how two processes are coordinated during replication. We propose that the Dpb3-Dpb4 heterodimer together with Cdc20 serves as a platform for the recruitment of chromatin modifiers and remodelers that mediate heterochromatin assembly during DNA replication, and ensure the faithful inheritance of epigenetic marks in heterochromatin.
PubMed: 29109278
DOI: 10.1073/pnas.1712961114
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.9 Å)
Structure validation

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数据于2025-07-30公开中

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