Structural Insights of the Ssdna Binding Site in the Multifunctional Endonuclease Atbfn2 from Arabidopsis Thaliana.Yu, T., Maestre-Reyna, M., Ko, C., Ko, T., Sun, Y., Lin, T., Shaw, J., Wang, A.H.
(2014) Plos One 9: 05821
- PubMed: 25157844
- DOI: 10.1371/journal.pone.0105821
- Primary Citation of Related Structures:
- PubMed Abstract:
The multi S1/P1 nuclease AtBFN2 (EC 18.104.22.168) 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 add ...
The multi S1/P1 nuclease AtBFN2 (EC 22.214.171.124) 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.
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.