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M205235200v1
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Papers In Press, published online ahead of print July 29, 2002
J. Biol. Chem, 10.1074/jbc.M205235200
Submitted on May 28, 2002
Revised on July 20, 2002
Accepted on July 26, 2002

Molecular structure and novel DNA binding sites located in loops of flap endonuclease-1

Eriko Matsui, Krishnasastry V. Musti, Junko Abe, Kazuhiko Yamasaki, Ikuo Matsui, and Kazuaki Harata

Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566

Corresponding Author: ik-matsui{at}aist.go.jp

The crystal structure of flap endonuclease-1 (phFEN-1) from Pyrococcus horikoshii was determined to a resolution of 3.1 Å. The active cleft of phFEN-1 molecule is formed with one large loop and four small loops. We examined the function of the conserved residues and positively charged clusters on these loops by kinetic analysis with 45 different mutants. R40R42 on small loop 1, a cluster K193-K195 on small loop 2, and two sites, R94, and R118 K119 on the large loop were identified as binding sites. K87 on the large loop may play significant roles in catalytic reaction. Furthermore, we successfully elucidated the function of the four DNA binding sites which form productive ES complexes specific for each endo- or exo-type hydrolysis, probably by bending the substrates. For the endo-activity, R94 and K193-K195 located at the top and bottom of the molecule were key determinants. For the exo-activity, all four sites were needed, but R118K119 was dominant. The major binding sites for both the nick substrate and dsDNA might be the same.


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