Flap endonuclease 1

Abstract

First discovered as a structure-specific endonuclease that evolved to cut at the base of single-stranded flaps, flap endonuclease (FEN1) is now recognized as a central component of cellular DNA metabolism. Substrate specificity allows FEN1 to process intermediates of Okazaki fragment maturation, long-patch base excision repair, telomere maintenance, and stalled replication fork rescue. For Okazaki fragments, the RNA primer is displaced into a 5' flap and then cleaved off. FEN1 binds to the flap base and then threads the 5' end of the flap through its helical arch and active site to create a configuration for cleavage. The threading requirement prevents this active nuclease from cutting the single-stranded template between Okazaki fragments. FEN1 efficiency and specificity are critical to the maintenance of genome fidelity. Overall, recent advances in our knowledge of FEN1 suggest that it was an ancient protein that has been fine-tuned over eons to coordinate many essential DNA transactions.

Figure 1

Flap endonuclease 1 (FEN1) substrate recognition and cleavage. FEN1 (a) recognizes the displaced flap, (b) binds to the base of the flap, (c) bends the substrate into a 100° angle to arrange the one-nucleotide 3′ overhang and 5′ displaced flap in the active site, and (d) precisely cleaves the flap, generating a nick. Based on structure information from Reference 41 and adapted with permission from Susan E. Tsutakawa, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.

Figure 2

Alternate FEN1 cleavage. Substrates with trinucleotide repeats or other self-complementary sequences can equilibrate to contain (a) both 5′ and 3′flaps, (b)only a 5′ flap, or (c) a configuration producing an expansion intermediate by creating a hairpin and a flap with an alternate FEN1 cleavage site. The green arrows indicate the sites of FEN1 cleavage.