4CXV

Structure of bifunctional endonuclease (AtBFN2) in complex with phosphate.

Summary for 4CXV

• Entry DOI: 10.2210/pdb4cxv/pdb
• Related: 4CWM 4CXO 4CXP
• Descriptor: ENDONUCLEASE 2, alpha-D-mannopyranose-(1-3)-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, ... (9 entities in total)
• Functional Keywords: hydrolase, ssdna binding
• Biological source: ARABIDOPSIS THALIANA (THALE CRESS)
• Total number of polymer chains: 2
• Total formula weight: 65272.91

Authors

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. (deposition date: 2014-04-09, release date: 2014-07-23, Last modification date: 2024-11-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2 Å)