An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA

Endonuclease IV (EndoIV) is an endonuclease that acts at apurinic/apyrimidinic (AP) sites and is classified as either long‐type or short‐type. The crystal structures of representative types of EndoIV from Geobacillus kaustophilus and Thermus thermophilus HB8 were determined using X‐ray crystallography. G. kaustophilus EndoIV (the long type) had a higher affinity for double‐stranded DNA containing an AP‐site analogue than T. thermophilus EndoIV (the short type). Structural analysis of the two different EndoIVs suggested that a C‐terminal DNA‐recognition loop that is only present in the long type contributes to its high affinity for AP sites. A mutation analysis showed that Lys267 in the C‐terminal DNA‐recognition loop plays an important role in DNA binding.