2A8G image
Entry Detail
PDB ID:
2A8G
Title:
Structure of Avidin in complex with the ligand deoxyguanosine
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2005-07-08
Release Date:
2006-05-23
Method Details:
Experimental Method:
Resolution:
1.99 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.23
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Avidin
Chain IDs:A, B
Chain Length:126
Number of Molecules:2
Biological Source:Gallus gallus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
Primary Citation
Recognition of oxidatively modified bases within the biotin-binding site of avidin.
J.Mol.Biol. 357 263 274 (2006)
PMID: 16413579 DOI: 10.1016/j.jmb.2005.12.054

Abstact

Oxidative damage of DNA results in the formation of many products, including 8-oxodeoxyguanosine, which has been used as a marker to quantify DNA damage. Earlier studies have demonstrated that avidin, a protein prevalent in egg-white and which has high affinity for the vitamin biotin, binds to 8-oxodeoxyguanosine and related bases. In this study, we have determined crystal structures of avidin in complex with 8-oxodeoxyguanosine and 8-oxodeoxyadenosine. In each case, the base is observed to bind within the biotin-binding site of avidin. However, the mode of association between the bases and the protein varies and, unlike in the avidin:biotin complex, complete ordering of the protein in this region does not accompany binding. Fluorescence studies indicate that in solution the individual bases, and a range of oligonucleotides, bind to avidin with micromolar affinity. Only one of the modes of binding observed is consistent with recognition of oxidised purines when incorporated within a DNA oligomer, and from this structure a model is proposed for the selective binding of avidin to DNA containing oxidatively damaged deoxyguanosine. These studies illustrate the molecular basis by which avidin might act as a marker of DNA damage, although the low levels of binding observed are inconsistent with the recognition of oxidised purines forming a major physiological role for avidin.

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Primary Citation of related structures