Cellular DNA is spontaneously and continuously damaged by environmental and internal factors such as X-rays, UV light and agents such as the antitumor drugs bleomycin and neocarzinostatin or those that generate oxygen radicals. Apurinic/apyrimidinic (AP) sites form both spontaneously and as highly cytotoxic intermediates in the removal of the damaged base by the base excision repair (BER) pathway. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3'terminus of DNA strand breaks.

AP endonucleases can be classified into two families on the basis of sequence similarity and structure (cf. family 1 <PDOC00598>). What we call family 2 groups the enzymes listed below [1,2].

• Bacterial endonuclease IV (gene nfo) (EC 3.1.21.2).
• Fungal and Caenorhabditis elegans apurinic endonuclase APN1 (EC 4.2.99.18).
• Dictyostelium endonuclease 4 homolog (EC 3.1.21.2).
• Archaeal probable endonuclease 4 homologs (EC 3.1.21.2).
• Mimivirus putative endonuclease 4 (EC 3.1.21.2).

APN1 and nfo have been shown to be transition metalloproteins that bind three zinc ions [3,4]. The metal-binding sites have been determined from the 3D-structure of Escherichia coli nfo [4,6,7], which shows an α/β-barrel fold (see <PDB:1QTW; A>) similar to that of other divalent metal-dependent TIM barrel enzymes (see <PDOC00155>), such as xylose isomerase (see <PDOC00156>).

We developed three signature patterns for this family of enzymes. The patterns are based on regions that contain conserved residues involved in zinc-binding. We also developed a profile that covers the entire AP endonuclease family 2 structure.