5GVD

Human TDRD3 DUF1767-OB domains

Summary for 5GVD

• Entry DOI: 10.2210/pdb5gvd/pdb
• Related: 5GVC 5GVE
• Descriptor: Tudor domain-containing protein 3, PHOSPHATE ION, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: scaffold protein, protein binding
• Biological source: Homo sapiens (Human)
• Cellular location: Cytoplasm : Q9H7E2
• Total number of polymer chains: 2
• Total formula weight: 35957.09

Authors

Goto-Ito, S.,Yamagata, A.,Sato, Y.,Takahashi, T.S.,Fukai, S. (deposition date: 2016-09-05, release date: 2017-06-14, Last modification date: 2023-11-08)

Primary citation

Goto-Ito, S.,Yamagata, A.,Takahashi, T.S.,Sato, Y.,Fukai, S.
Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7:42123-42123, 2017

PubMed Abstract: Topoisomerase IIIβ (TOP3β) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3β co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recruit TOP3β to its DNA/RNA substrates accumulating in specific cellular sites such as methylated chromatins or neural stress granules. Here we report the crystal structures of the catalytic domain of TOP3β, the DUF1767-OB-fold domains of TDRD3 and their complex at 3.44 Å, 1.62 Å and 3.6 Å resolutions, respectively. The toroidal-shaped catalytic domain of TOP3β binds the OB-fold domain of TDRD3. The TDRD3 OB-fold domain harbors the insertion loop, which is protruding from the core structure. Both the insertion loop and core region interact with TOP3β. Our pull-down binding assays showed that hydrophobic characters of the core surface and the amino- and carboxy-terminal regions of the insertion loop are essential for the interaction. Furthermore, by comparison with the structure of the homologous Topoisomerase IIIα (TOP3α)-RMI1 complex, we identified Arg96, Val109, Phe139 and the short insertion loop of TDRD3 as the critical structural elements for the specific interaction with TOP3β to avoid the non-cognate interaction with TOP3α.

PubMed: 28176834
DOI: 10.1038/srep42123

Experimental method

X-RAY DIFFRACTION (1.623 Å)