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PDBsum entry 1kfv
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Hydrolase/DNA
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PDB id
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1kfv
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the lactococcus lactis formamidopyrimidine-Dna glycosylase bound to an abasic site analogue-Containing DNA.
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Authors
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L.Serre,
K.Pereira de jésus,
S.Boiteux,
C.Zelwer,
B.Castaing.
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Ref.
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EMBO J, 2002,
21,
2854-2865.
[DOI no: ]
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PubMed id
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Abstract
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The formamidopyrimidine-DNA glycosylase (Fpg, MutM) is a bifunctional base
excision repair enzyme (DNA glycosylase/AP lyase) that removes a wide range of
oxidized purines, such as 8-oxoguanine and imidazole ring-opened purines, from
oxidatively damaged DNA. The structure of a non-covalent complex between the
Lactoccocus lactis Fpg and a 1,3-propanediol (Pr) abasic site
analogue-containing DNA has been solved. Through an asymmetric interaction along
the damaged strand and the intercalation of the triad (M75/R109/F111), Fpg
pushes out the Pr site from the DNA double helix, recognizing the cytosine
opposite the lesion and inducing a 60 degrees bend of the DNA. The specific
recognition of this cytosine provides some structural basis for understanding
the divergence between Fpg and its structural homologue endo nuclease VIII
towards their substrate specificities. In addition, the modelling of the
8-oxoguanine residue allows us to define an enzyme pocket that may accommodate
the extrahelical oxidized base.
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Figure 6.
Figure 6 Stereo view of Fpg contacts around the Pr abasic site
analogue. Hydrogen bonds are indicated by dashed lines. DNA
atoms are represented by orange ball-and-sticks, and mutagenesis
targeted amino acids are underlined (see text for details). The
figures were generated by Molscript (Kraulis et al., 1991) and
Raster3-D (Merritt and Murphy, 1994).
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Figure 8.
Figure 8 Recognition of the C20 opposite the Pr site by R109.
Stereo view showing the intercalation of the Fpg triad by the
minor groove and the pseudo-Watson−Crick interactions between
R109 and C20. Hydrogen bonds are indicated by dashed lines. The
atomic coordinates of the triad (M70/R99/F101) from the free
TtFpg have been superposed and are represented by green
ball-and-sticks. The figure was generated by Molscript (Kraulis
et al., 1991) and Raster3-D (Merritt and Murphy, 1994).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
2854-2865)
copyright 2002.
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