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PDBsum entry 3cvs

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Top Page protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
3cvs
Jmol
Contents
Protein chains
282 a.a.
DNA/RNA
Waters ×167

References listed in PDB file
Key reference
Title 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.
Authors B.R.Bowman, S.Lee, S.Wang, G.L.Verdine.
Ref. Structure, 2008, 16, 1166-1174. [DOI no: 10.1016/j.str.2008.04.012]
PubMed id 18682218
Abstract
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.
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.
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.
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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