8WMS image
Deposition Date 2023-10-04
Release Date 2024-07-31
Last Version Date 2025-03-19
Entry Detail
PDB ID:
8WMS
Keywords:
Title:
Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.26
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
I 41 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase UHRF1
Gene (Uniprot):UHRF1
Chain IDs:A
Chain Length:68
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Developmental pluripotency-associated protein 3
Gene (Uniprot):DPPA3
Chain IDs:B
Chain Length:38
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structure of human DPPA3 bound to the UHRF1 PHD finger reveals its functional and structural differences from mouse DPPA3.
Commun Biol 7 746 746 (2024)
PMID: 38898124 DOI: 10.1038/s42003-024-06434-9

Abstact

DNA methylation maintenance is essential for cell fate inheritance. In differentiated cells, this involves orchestrated actions of DNMT1 and UHRF1. In mice, the high-affinity binding of DPPA3 to the UHRF1 PHD finger regulates UHRF1 chromatin dissociation and cytosolic localization, which is required for oocyte maturation and early embryo development. However, the human DPPA3 ortholog functions during these stages remain unclear. Here, we report the structural basis for human DPPA3 binding to the UHRF1 PHD finger. The conserved human DPPA3 85VRT87 motif binds to the acidic surface of UHRF1 PHD finger, whereas mouse DPPA3 binding additionally utilizes two unique α-helices. The binding affinity of human DPPA3 for the UHRF1 PHD finger was weaker than that of mouse DPPA3. Consequently, human DPPA3, unlike mouse DPPA3, failed to inhibit UHRF1 chromatin binding and DNA remethylation in Xenopus egg extracts effectively. Our data provide novel insights into the distinct function and structure of human DPPA3.

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Primary Citation of related structures