Biology Reference
In-Depth Information
presence of lesion-containing DNA in a complex with catalytically inactive
enzymes, the density for this loop resurfaces, indicating conformational mobil-
ity upon catalysis.
59,64,65
This loop plays a key role in the recognition of 8-oxoG:
a projection from the loop wraps around the damaged base forming an exten-
sive network of hydrogen bonds.
59
This same loop was shown to wrap around
FapyG in the LlaFpg structure.
60
The major difference between the binding of
Fpg to 8-oxoG and FapyG lies in the fact that binding in the extrahelical base-
binding pocket of Fpg for the former lesion occurs in the
syn
conformation,
whereas FapyG is in the
anti
conformation. However, despite the difference in
base conformations, a similar type of interaction exists between the main-chain
carbonyl carbons of conserved residues S218 (in LlaFpg) and S221 (in BstFpg),
which bind to the protonated N1 and N7 of FapyG and 8-oxoG, respectively.
Similarly, the conserved I220 (in LlaFpg) and the analogous V223 (in BstFpg)
use their main-chain amide group for hydrogen bonding with the carbonyl
moiety at position 6 of both lesions.
60
The
9/10 loops of bacterial Fpgs are functionally similar and are of
comparable length (
a
F-
b
27 residues) and conformation. In contrast, in the eukar-
yotic members of the family, which do not recognize 8-oxoG, this putative
lesion-recognition loop is generally shorter or even missing as in the case of
NEIL1,
61
AthFpg (St ´phanie Duclos, Pierre Aller, Pawel Jaruga, Miral Did-
zaroglu, Susan S. Wallace and Sylvie Doubli ´ , Manuscript submitted to DNA
Repair). A superposition of BstFpg bound to DNA (containing 8-oxoG:C
59
)
with the unliganded human NEIL1
61
and the MvNei1 enzymes illustrates that
this loop wraps around the lesion only in the case of BstFpg (
Fig. 3
). In
contrast, in the case of NEIL1, the loop is replaced by an
-helix and the
loop is shorter in MvNei1; in both cases, this segment is unable to wrap around
the lesion (
Fig. 3
). These data are consistent with the fact that 8-oxoG is not a
good substrate for NEIL1 or any of the eukaryotic and mimivirus enzymes that
are missing this loop. In fact, deletion of the
a
9/10 loop in EcoFpg yielded a
variant that retains catalytic ability on oxidized pyrimidines and FapyG, but not
8-oxoG, implying that this loop is important for stabilizing 8-oxoG and not the
other lesions (St
´
phanie Duclos, Pierre Aller, Pawel Jaruga, Miral Didzaroglu,
Susan S. Wallace and Sylvie Doubli
´
, Manuscript submitted to DNA Repair).
The bacterial Nei proteins are composed of members that share several
characteristics with Fpg but also provide some unique variations. The crystal
structure of EcoNei reveals a similar structural fold and conservation of motifs
present in the Fpg proteins.
56,62
A striking difference between the unliganded
and DNA-bound EcoNei structures is a large conformational change of about
50
between the N- and C-terminal domains. This is the only DNA glycosylase
to date that has been reported to display a DNA-induced global conformational
change, in which the glycosylase transforms from an elongated ''open'' form to a
''closed'' DNA-bound form.
56,62
This conformational change was not observed
for the MvNei1 protein upon DNA binding.
67
a
F-
b
