3M7D

Crystal structure of an N-terminal 44 kDA fragment of topoisomerase V in the presence of dioxane

Summary for 3M7D

• Entry DOI: 10.2210/pdb3m7d/pdb
• Related: 3M6K 3M6Z 3M7G
• Descriptor: Topoisomerase V (2 entities in total)
• Functional Keywords: helix-hairpin-helix, topoisomerase, conformational change, isomerase
• Biological source: Methanopyrus kandleri
• Total number of polymer chains: 1
• Total formula weight: 44232.01

Authors

Rajan, R.,Taneja, B.,Mondragon, A. (deposition date: 2010-03-16, release date: 2010-08-04, Last modification date: 2024-11-27)

Primary citation

Rajan, R.,Taneja, B.,Mondragon, A.
Structures of minimal catalytic fragments of topoisomerase v reveals conformational changes relevant for DNA binding.
Structure, 18:829-838, 2010

PubMed Abstract: Topoisomerase V is an archaeal type I topoisomerase that is unique among topoisomerases due to presence of both topoisomerase and DNA repair activities in the same protein. It is organized as an N-terminal topoisomerase domain followed by 24 tandem helix-hairpin-helix (HhH) motifs. Structural studies have shown that the active site is buried by the (HhH) motifs. Here we show that the N-terminal domain can relax DNA in the absence of any HhH motifs and that the HhH motifs are required for stable protein-DNA complex formation. Crystal structures of various topoisomerase V fragments show changes in the relative orientation of the domains mediated by a long bent linker helix, and these movements are essential for the DNA to enter the active site. Phosphate ions bound to the protein near the active site helped model DNA in the topoisomerase domain and show how topoisomerase V may interact with DNA.

PubMed: 20637419
DOI: 10.1016/j.str.2010.03.006

Experimental method

X-RAY DIFFRACTION (1.815 Å)