2A5C

Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine

Summary for 2A5C

• Entry DOI: 10.2210/pdb2a5c/pdb
• Descriptor: Avidin, 2-acetamido-2-deoxy-beta-D-glucopyranose, 8-OXODEOXYADENOSINE, ... (4 entities in total)
• Functional Keywords: avidin, damaged dna, 8-oxodeoxyadenosine, unknown function
• Biological source: Gallus gallus (chicken)
• Cellular location: Secreted: P02701
• Total number of polymer chains: 2
• Total formula weight: 28391.65

Authors

Conners, R.,Hooley, E.,Thomas, S.,Brady, R.L. (deposition date: 2005-06-30, release date: 2006-05-23, Last modification date: 2024-11-13)

Primary citation

Conners, R.,Hooley, E.,Clarke, A.R.,Thomas, S.,Brady, R.L.
Recognition of oxidatively modified bases within the biotin-binding site of avidin.
J.Mol.Biol., 357:263-274, 2006

PubMed Abstract: 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.

PubMed: 16413579
DOI: 10.1016/j.jmb.2005.12.054

Experimental method

X-RAY DIFFRACTION (2.5 Å)