4CWM

High-glycosylation crystal structure of the bifunctional endonuclease (AtBFN2) from Arabidopsis thaliana

4CWM の概要

• エントリーDOI: 10.2210/pdb4cwm/pdb
• 分子名称: ENDONUCLEASE 2, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• 機能のキーワード: hydrolase, ssdna binding
• 由来する生物種: ARABIDOPSIS THALIANA (THALE CRESS)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 65448.30

構造登録者

Yu, T.-F.,Maestre-Reyna, M.,Ko, C.-Y.,Ko, T.-P.,Sun, Y.-J.,Lin, T.-Y.,Shaw, J.-F.,Wang, A.H.-J. (登録日: 2014-04-03, 公開日: 2014-07-23, 最終更新日: 2024-10-23)

主引用文献

Yu, T.,Maestre-Reyna, M.,Ko, C.,Ko, T.,Sun, Y.,Lin, T.,Shaw, J.,Wang, A.H.
Structural Insights of the Ssdna Binding Site in the Multifunctional Endonuclease Atbfn2 from Arabidopsis Thaliana.
Plos One, 9:05821-, 2014

PubMed Abstract: The multi S1/P1 nuclease AtBFN2 (EC 3.1.30.1) encoded by the Arabidopsis thaliana At1g68290 gene is a glycoprotein that digests RNA, ssDNA, and dsDNA. AtBFN2 depends on three zinc ions for cleaving DNA and RNA at 3'-OH to yield 5'-nucleotides. In addition, AtBFN2's enzymatic activity is strongly glycan dependent. Plant Zn(2+)-dependent endonucleases present a unique fold, and belong to the Phospholipase C (PLC)/P1 nuclease superfamily. In this work, we present the first complete, ligand-free, AtBFN2 crystal structure, along with sulfate, phosphate and ssDNA co-crystal structures. With these, we were able to provide better insight into the glycan structure and possible enzymatic mechanism. In comparison with other nucleases, the AtBFN2/ligand-free and AtBFN2/PO4 models suggest a similar, previously proposed, catalytic mechanism. Our data also confirm that the phosphate and vanadate can inhibit the enzyme activity by occupying the active site. More importantly, the AtBFN2/A5T structure reveals a novel and conserved secondary binding site, which seems to be important for plant Zn(2+)-dependent endonucleases. Based on these findings, we propose a rational ssDNA binding model, in which the ssDNA wraps itself around the protein and the attached surface glycan, in turn, reinforces the binding complex.

PubMed: 25157844
DOI: 10.1371/JOURNAL.PONE.0105821

実験手法

X-RAY DIFFRACTION (2.09 Å)