Yu T.-FMANUEL MAESTRE-REYNAKo C.-YKo T.-PSun Y.-JLin T.-YShaw J.-FWang A.H.-J.2022-11-112022-11-11201419326203https://www.scopus.com/inward/record.uri?eid=2-s2.0-84940344933&doi=10.1371%2fjournal.pone.0105821&partnerID=40&md5=8e1ae2295e32006577c8d0bfe08f863fhttps://scholars.lib.ntu.edu.tw/handle/123456789/624881The 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 Zn2+-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. © 2014 Yu et al.double stranded DNA; endonuclease; endonuclease AtBFN2; glycan; glycoprotein; nuclease; phosphate; phospholipase C; RNA; single stranded DNA; sulfate; unclassified drug; vanadic acid; Arabidopsis protein; coordination compound; ENDO2 protein, Arabidopsis; endonuclease; phosphate; single stranded DNA; sulfate; zinc; Arabidopsis thaliana; article; binding site; crystal structure; crystallization; DNA cleavage; DNA structure; enzyme activity; humidity; mutagenesis; nonhuman; protein folding; protein purification; RNA cleavage; seedling; X ray diffraction; amino acid sequence; Arabidopsis; chemical structure; chemistry; enzyme active site; enzymology; molecular genetics; X ray crystallography; Amino Acid Sequence; Arabidopsis; Arabidopsis Proteins; Catalytic Domain; Coordination Complexes; Crystallography, X-Ray; DNA, Single-Stranded; Endonucleases; Models, Molecular; Molecular Sequence Data; Phosphates; Sulfates; Zincjournal article10.1371/journal.pone.0105821251578442-s2.0-84940344933