Final answer:
The enzyme phosphodiesterase removes the single empty sugar phosphate residue after DNA glycosylase excision and AP endonuclease nicking, with DNA polymerase and DNA ligase III completing the repair process.
Step-by-step explanation:
The removal of a single empty sugar phosphate residue from DNA is accomplished through a coordinated series of enzymatic reactions. After DNA glycosylase removes a damaged or incorrect base, AP endonuclease nicks the DNA backbone at the site of the abasic sugar (the sugar that has lost its base). This creates an entry point for phosphodiesterase to hydrolyze the phosphodiester bond, effectively removing the sugar phosphate residue. Finally, DNA polymerase adds the correct nucleotide to the 3' end of the resulting gap, and DNA ligase III seals the nick, restoring the integrity of the DNA strand. This process is vital for DNA repair and is an example of the extraordinary mechanisms cells use to maintain genetic fidelity.