Mechanistic insights to catalysis by a zinc-dependent bi-functional nuclease from Arabidopsis thaliana

•The crystal structure of AtBFN2 was determined at 1.76-Å resolution.•The mostly α-helical protein contains five short β-strands and four disulfides.•Three N-linked oligosaccharide chains were attached to Asn91, Asn110 and Asn184.•The active site showed a sulfate bound to three zinc ions, and an adenine base.•The structure supports an in-line attack catalytic mechanism.

The bi-functional nuclease AtBFN2 from Arabidopsis thaliana (EC 3.1.30.1) depends on zinc ion for cleaving single stranded DNA and RNA to yield 5′-nucleotides. It is a glycoprotein that participates in plant development and differentiation. The crystal structure of AtBFN2 shows a bound sulfate ion in the active site, at the center of the tri-nuclear cluster of zinc ions. The protein folds into a mostly α-helical structure with five short β-strands and contains four disulfide bonds. The zinc ions are coordinated to the side chains of three Asp and five His residues, two backbone atoms of Trp1, the sulfate ion, and a water molecule. An adenine base is bound adjacent to the active site and stacks with Tyr59. The core sugar residues attached to the three N-glycosylation sites of Asn91, Asn110 and Asn184 are also observed. By comparison with the nuclease P1 structure (PDB ID: 1AK0), the AtBFN2-sulfate-adenine complex model suggests a similar catalytic mechanism, in which the reaction starts with in-line attack at the phosphate by a zinc-activated water molecule.