5HX4

Zinc-Free APOBEC3F Catalytic Domain Crystal Structure

5HX4 の概要

• エントリーDOI: 10.2210/pdb5hx4/pdb
• 関連するPDBエントリー: 5HX5
• 分子名称: DNA dC->dU-editing enzyme APOBEC-3F (2 entities in total)
• 機能のキーワード: apobec3f, hydrolase
• 由来する生物種: Homo sapiens (Human)
• 細胞内の位置: Cytoplasm: Q8IUX4
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 46722.16

構造登録者

Shaban, N.M.,Shi, K.,Aihara, H.,Harris, R.S. (登録日: 2016-01-29, 公開日: 2016-05-18, 最終更新日: 2024-11-20)

主引用文献

Shaban, N.M.,Shi, K.,Li, M.,Aihara, H.,Harris, R.S.
1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure.
J.Mol.Biol., 428:2307-2316, 2016

PubMed Abstract: The APOBEC3 family of DNA cytosine deaminases is capable of restricting the replication of HIV-1 and other pathogens. Here, we report a 1.92 Å resolution crystal structure of the Vif-binding and catalytic domain of APOBEC3F (A3F). This structure is distinct from the previously published APOBEC and phylogenetically related deaminase structures, as it is the first without zinc in the active site. We determined an additional structure containing zinc in the same crystal form that allows direct comparison with the zinc-free structure. In the absence of zinc, the conserved active site residues that normally participate in zinc coordination show unique conformations, including a 90 degree rotation of His249 and disulfide bond formation between Cys280 and Cys283. We found that zinc coordination is influenced by pH, and treating the protein at low pH in crystallization buffer is sufficient to remove zinc. Zinc coordination and catalytic activity are reconstituted with the addition of zinc only in a reduced environment likely due to the two active site cysteines readily forming a disulfide bond when not coordinating zinc. We show that the enzyme is active in the presence of zinc and cobalt but not with other divalent metals. These results unexpectedly demonstrate that zinc is not required for the structural integrity of A3F and suggest that metal coordination may be a strategy for regulating the activity of A3F and related deaminases.

PubMed: 27139641
DOI: 10.1016/j.jmb.2016.04.026

実験手法

X-RAY DIFFRACTION (1.92 Å)