Structural Insights into the Mechanism of Nuclease A, a ββα Metal Nuclease from Anabaena*

Nuclease A (NucA) is a nonspecific endonuclease from Anabaena sp. capable of degrading single- and double-stranded DNA and RNA in the presence of divalent metal ions. We have determined the structure of the Δ(2-24),D121A mutant of NucA in the presence of Zn²⁺ and Mn²⁺ (PDB code 1ZM8). The mutations were introduced to remove the N-terminal signal peptide and to reduce the activity of the nonspecific nuclease, thereby reducing its toxicity to the Escherichia coli expression system. NucA contains a ββα metal finger motif and a hydrated Mn²⁺ ion at the active site. Unexpectedly, NucA was found to contain additional metal binding sites ∼26 Å apart from the catalytic metal binding site. A structural comparison between NucA and the closest analog for which structural data exist, the Serratia nuclease, indicates several interesting differences. First, NucA is a monomer rather than a dimer. Second, there is an unexpected structural homology between the N-terminal segments despite a poorly conserved sequence, which in Serratia includes a cysteine bridge thought to play a regulatory role. In addition, although a sequence alignment had suggested that NucA lacks a proposed catalytic residue corresponding to Arg⁵⁷ in Serratia, the structure determined here indicates that Arg⁹³ in NucA is positioned to fulfill this role. Based on comparison with DNA-bound nuclease structures of the ββα metal finger nuclease family and available mutational data on NucA, we propose that His¹²⁴ acts as a catalytic base, and Arg⁹³ participates in the catalysis possibly through stabilization of the transition state.