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characteristic of the disordered tails in DNA-binding proteins is clustering
of positively charged residues in the distal region, which were shown to be
important for the scanning. Mutating such residues in HOXD9 and NK-2
markedly decreases the scanning efficiency.
109,112
Similar results were
obtained when the N-terminal segment in these proteins were deleted,
suggesting that the initial scanning is mediated by a nonspecific, mostly
electrostatic transient DNA binding via the basic disordered segment,
which is followed by target DNA sequence binding by the active site.
109,113
In light of these studies, we examined hNEIL1's C terminus, which pos-
sesses most of the characteristics required for DNA scanning, including the
presence of clustered basic residues. Our recent biochemical studies using
C-terminal deletion mutants of NEIL1 showed that the C terminus is impor-
tant for NEIL1's substrate scanning and efficiency of damage recognition, via
its nonspecific DNA binding (Hegde ML and Mitra S, unpublished data).
Although limited information is available on the role of disordered regions in
other early BER proteins, we predict a similar situation for these proteins as
observed for NEIL1 or APE1.
IV. Posttranslational Modifications in Early BER Proteins
Posttranslational modifications of proteins, including acetylation, phos-
phorylation, ubiquitylation, ADP-ribosylation, sumoylation, and methylation,
play a critical role in diverse cellular processes including DNA repair.
114
Such
covalent modifications may have multiple physiological effects on these pro-
teins, including stability, interaction with DNA or other proteins, organelle
targeting, and enzymatic activity.
115
Furthermore, the modification sites are
often localized in disordered regions, for example, in the N-terminal segment
in hAPE1,
116,117
N and C termini of p53,
118
and the C-terminal region in
hNEIL1 (Bhakat KK, Hegde ML and Mitra S, unpublished data).
A. Acetylation and Phosphorylation Modulate Repair
Activity
The functions of DNA repair proteins are generally regulated via their
acetylation or phosphorylation. These modifications could also regulate protein
stability, interaction, and intracellular distribution (reviewed in
Ref. 115
). Our
laboratories and others identified and characterized acetylation of hAPE1 at
Lys6 or Lys7, Lys25, Lys27, and Lys31,
116,119
Lys 6 and 7 acetylation strongly
affects APE1's transcriptional regulatory functions.
116
APE1 stably interacts
with Y-box-binding protein 1 (YB-1) and acetylation further enhances its
