STRUCTURAL AND FUNCTIONAL-ANALYSIS OF THE HOMING ENDONUCLEASE PI-SCEIBY LIMITED PROTEOLYTIC CLEAVAGE AND MOLECULAR-CLONING OF PARTIAL DIGESTION PRODUCTS
V. Pingoud et al., STRUCTURAL AND FUNCTIONAL-ANALYSIS OF THE HOMING ENDONUCLEASE PI-SCEIBY LIMITED PROTEOLYTIC CLEAVAGE AND MOLECULAR-CLONING OF PARTIAL DIGESTION PRODUCTS, Biochemistry, 37(22), 1998, pp. 8233-8243
PI-SceI is a member of an unusual class of rare cutting homing endonuc
leases produced by an autocatalytic protein splicing from a precursor.
To analyze the structural and functional domain organization of the e
ndonuclease PI-SceI and to examine whether the DNA binding activity ca
n be structurally separated from the catalytic activity, we performed
limited proteolytic digestion experiments with various proteases. Two
protease-resistant fragments spanning the N- and C-terminal halves of
the nuclease were identified using different proteases which cleave th
e protein in the same region, Each fragment contains one of the two co
nserved LAGLIDADG motifs. The products of the limited proteolytic dige
sts were shown to remain associated and to exhibit specific DNA bindin
g but to be inactive in DNA cleavage. Different from what is observed
with native PI-SceI, only one complex is formed as shown in an electro
phoretic mobility shift assay. Expression clones for the N- and C-term
inal protein fragments obtained by tryptic digestion were constructed,
and the proteins PI-SceI-N and PI-SceI-C were purified. Only PI-SceI-
N exhibits DNA binding activity. Bending experiments with:PI-SceI-N, a
mixture of PI-SceI-N and PI-SceI-C, as well as the products of the li
mited tryptic digest show that a DNA substrate with the full length re
cognition sequence is bent by 45 degrees. This degree of bending is al
so observed with a DNA containing only the right side of the recogniti
on sequence, corresponding to one of the DNA cleavage products of PI-S
ceI. Our results demonstrate that the N-terminal half of PI-SceI which
lacks one of the two LAGLDADG motifs is able to bind to DNA specifica
lly and to induce one of the distortions observed to occur in the proc
ess of DNA binding by PI-SceI. These results are discussed in light of
the recently solved crystal structure of PI-SceI and used to refine a
model for the mechanism of DNA binding and cleavage by PI-SceI.