Biology Reference
In-Depth Information
B. Substrate Preference
Bacterial Fpg proteins characteristically excise oxidized purines, whereas
bacterial Nei and the Neil proteins excise oxidized pyrimidines (for reviews
see Refs.
28,29,34,71,72
). Interestingly, the Fpg proteins share similar substrate
specificity with Ogg, whereas the substrate specificity of the Nei family mem-
bers overlaps with that of the Nth family. However, all Fpg/Nei family members
share sequence homology. Glycosylases vary in their discrimination of the bases
opposite the lesion as well as their preference for the nature of the DNA, that is,
single-stranded DNA, double-stranded DNA, or bubble-containing substrates.
Fpg primarily exhibits a substrate preference for purines such as 8-oxoG and
FapyG, although oxidized pyrimidines are also removed,
86,87
whereas bacterial
Nei and the rest of the eukaryotic family members such as NEIL1 and NEIL2
recognize a wider array of substrates.
Recently, it was determined that EcoFpg is more efficient at removing
spiroiminodihydantoin (Sp), a further oxidation product of 8-oxoG, from
double-stranded DNA substrates than 8-oxoG itself.
73,88
EcoNei, like endonu-
clease III, recognizes Tg, dihydrothymine (DHT),
-ureidoisobutyric acid, and
urea residues (for reviews see Refs.
28,29,34,72,78
). EcoNei can also recognize
5-hydroxycytosine (5-OHC), 5-hydroxyuracil (5-OHU), and uracil glycol.
79
MvNei1 and NEIL1 share substrate preferences for oxidized pyrimidines in
duplex DNA and also recognize and process lesions from single-stranded
DNA.
80,82
Although 8-oxoG is not a preferred substrate for NEIL1, its further
oxidation products guanidinohydantoin (Gh) and Sp are both excellent
substrates for these enzymes when paired opposite C rather than A.
39,40,80
The NEIL1 protein also excises Tg, 5,6-dihydrouracil (DHU), FapyA, and
FapyG, as well as 5-OHU, 5-OHC, and oxanine.
30,31,81,89,90
Bacterial Fpg
91,92
and all the eukaryotic members of the Fpg/Nei family recognize lesions in
single-stranded DNA.
31,36,80
NEIL2 and MmuNeil3 prefer to excise lesions
present in single-stranded, bubble, or forked DNA structures over those in
duplex DNA.
24,36,39,42-44,48
b
C. Comparison of Structures of the Fpg/Nei Family
As mentioned earlier, currently there are crystal structures of Fpg proteins
from four bacterial species, namely TthFpg, EcoFpg, BstFpg, and
LlaFpg.
54,55,57-60,63-66,68,69
All four proteins share the same domain structure
and considerable sequence homology. Structures of intermediates covalently
linked to duplex DNA indicate that the DNA binds to the enzyme in a
positively charged groove that runs roughly orthogonal to the DNA axis.
55,59
Bacterial Fpg binds DNA in the minor groove and the damaged base is
extruded through the major groove. The DNA appears to be severely kinked
at the lesion point (
roll angle in the case of EcoFpg
55
) upon enzyme
66
