   3.1.99.B1 | endonucleases that remove 5' DNA sequences from a DNA structure called a DNA flap. The DNA flap structure occurs in double-stranded DNA containing a single-stranded break where the 5' portion of the downstream strand is too long and overlaps the 3' end of the upstream strand. Flap endonucleases cleave the downstream strand of the overlap flap structure precisely after the first base-paired nucleotide, creating a ligatable nick |
in a most likely reaction pathway (very similar to that recently proposed for ribonuclease H, EC 3.1.13.2) the rate-determining step is the SN2-like nucleophilic attack of a water to the scissile phosphate, which occurs concomitantly with its activation by the pro-Rp oxygen of the nucleobase flanking the scissile phosphate. Preactivation of the nucleophilic water. Scheme of different possible reaction mechanisms, overview |
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