Biology Reference
In-Depth Information
activity. Although NTH1 contains an Fe-S cluster, it serves only as an archi-
tectural element to position a loop containing positively charged residues near
the phosphodiester backbone of a target DNA molecule.
26,27
Nei family pro-
teins in
E. coli
and mammals (except NEIL1) contain Zn finger motifs, which
are involved in DNA binding.
28
Because DGs remove base lesions that usually
cause minor, or no, distortion in the DNA duplex, damaged base sensing is a
major challenge for the DG, particularly for lesions such as U with subtle
modifications.
8
The difficulty is more severe in mammalian genome because
the lesion is located in condensed chromatin. It should be mentioned that
although DGs are involved in the recognition of base lesions owing to their
affinity for a group of modified bases, other signaling factors may also be
involved that have not been extensively addressed.
The mechanism of base lesion excision involves extrahelical flipping of the
damaged nucleotide into the DG's recognition pocket.
29,30
All DGs studied so
far bind to the minor groove of DNA, kinking it at the site of damage, and flip the
lesion nucleotide out of the major groove of DNA.
29,30
Thus, only those lesions
that could be accommodated in the binding pocket after nucleotide flipping to
provide the necessary contacts and orientation for their excision are removed by
the DGs. ROS produce more than 20 major oxidized base lesions that are
repaired by only four (or five) DGs in human cells; thus, each DG acts on
subsets of base lesions.
4,8,31
It is likely that the plasticity of the catalytic pockets
of DGs allows an induced fit of diverse substrates. It appears that DGs invari-
ably have low turnover to compensate for their promiscuity. The properties of
oxidized base-specific DGs and their preferred substrates are listed in
Table II
.
C. SSBR: A DG-independent Variant of BER
Repair of ROS-induced SSBs shares the last three steps of the BER
pathway, namely, end cleaning, gap-filling, and nick sealing, although SSBR
could involve additional end-processing enzymes to remove various termini
produced by ROS.
(i)
Diverse end-processing for SSBR.
The end-processing of SSBs has
recently been shown to be more versatile than previously suggested. The
most common block at ROS-induced SSB is 3
0
phosphoglycolate (or
3
0
phosphoglycolaldehyde), which is removed by APE1.
36,37
Tyrosylpho-
sphodiesterase 1 (TDP1), another 3
0
end-processing enzyme, cleaves
Top1 (Tyr)-cross-linked to 3
0
P at the strand break generated by abortive
topoisomerase 1 (Top1) reaction. TDP1 also processes 3
0
phosphoglycolate
at DSBs.
38
The resulting 3
0
P is subsequently removed by PNKP,
39-42
which
also phosphorylates the 5
0
OH generated at an SSB. A unique 5
0
blocking
group is formed as intermediates during abortive DNA ligation, namely,
adenylate linked to the 5
0
P terminus at an SSB via a 5
0
5
0
pyrophosphate
bond. Aprataxin releases 5
0
AMP to restore the 5
0
P terminus.
43,44
Some
