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PDBsum entry 3cvs
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Hydrolase/DNA
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PDB id
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3cvs
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References listed in PDB file
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Key reference
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Title
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Structure of the e. Coli DNA glycosylase alka bound to the ends of duplex DNA: a system for the structure determination of lesion-Containing DNA.
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Authors
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B.R.Bowman,
S.Lee,
S.Wang,
G.L.Verdine.
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Ref.
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Structure, 2008,
16,
1166-1174.
[DOI no: ]
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PubMed id
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Abstract
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The constant attack on DNA by endogenous and exogenous agents gives rise to
nucleobase modifications that cause mutations, which can lead to cancer.
Visualizing the effects of these lesions on the structure of duplex DNA is key
to understanding their biologic consequences. The most definitive method of
obtaining such structures, X-ray crystallography, is troublesome to employ owing
to the difficulty of obtaining diffraction-quality crystals of DNA. Here, we
present a crystallization system that uses a protein, the DNA glycosylase AlkA,
as a scaffold to mediate the crystallization of lesion-containing duplex DNA. We
demonstrate the use of this system to facilitate the rapid structure
determination of DNA containing the lesion 8-oxoguanine in several different
sequence contexts, and also deoxyinosine and 1,N(6)-ethenoadenine, each
stabilized as the corresponding 2'-flouro analog. The structures of 8-oxoguanine
provide a correct atomic-level view of this important endogenous lesion in DNA.
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Figure 2.
Figure 2. Cα Superposition of the AlkA Azaribose LRC
Structure onto an AlkA/DNA Subunit from the AlkA HGC
The
rmsd of the LRC (the protein is colored cyan as in Figure 1B;
DNA colored white) onto the HGC subunit (colored as in Figure
1C) is 0.37 Å. The crimson dot denotes the position of the
phosphate that hydrogen bonds with the protein backbone at
positions 249 and 251 (yellow loop); this phosphate is the only
element of the otherwise naked central portion of the DNA that
is contacted by the protein. The major sites of protein:DNA
interaction are colored as in Figure 1C.
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Figure 5.
Figure 5. B-Form DNA Containing oxoG:dA or oxoG:dC Base Pairs
(A–C) The oxoG:C base pairs (left column) with oxoG in
the (A) one position, (B) six position, and (C) eight position
within the DNA duplex. In the right column, G:C structures in
the same positions within the DNA as the respective lesion are
shown.
(D) Structure of oxoG base paired with adenine. The
color scheme, F[o] − F[c] electron density map and hydrogen
bonding are represented as in Figure 3.
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Structure
(2008,
16,
1166-1174)
copyright 2008.
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