1ZM8

Apo Crystal structure of Nuclease A from Anabaena sp.

Summary for 1ZM8

• Entry DOI: 10.2210/pdb1zm8/pdb
• Descriptor: Nuclease, MANGANESE (II) ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: nuca, nuclease, metal dependent, hydrolase
• Biological source: Anabaena sp.
• Cellular location: Periplasm: P38446
• Total number of polymer chains: 1
• Total formula weight: 28922.82

Authors

Ghosh, M.,Meiss, G.,Pingoud, A.,London, R.E.,Pedersen, L.C. (deposition date: 2005-05-10, release date: 2005-06-21, Last modification date: 2023-08-23)

Primary citation

Ghosh, M.,Meiss, G.,Pingoud, A.,London, R.E.,Pedersen, L.C.
Structural Insights into the Mechanism of Nuclease A, a beta beta alpha Metal Nuclease from Anabaena.
J.Biol.Chem., 280:27990-27997, 2005

PubMed Abstract: 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 delta(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 betabeta alpha metal finger motif and a hydrated Mn2+ ion at the active site. Unexpectedly, NucA was found to contain additional metal binding sites approximately 26 A 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 betabeta alpha 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.

PubMed: 15897201
DOI: 10.1074/jbc.M501798200

Experimental method

X-RAY DIFFRACTION (1.9 Å)