2a5c: Difference between revisions
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'''Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine''' | {{Structure | ||
|PDB= 2a5c |SIZE=350|CAPTION= <scene name='initialview01'>2a5c</scene>, resolution 2.500Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene> and <scene name='pdbligand=8DA:8-OXODEOXYADENOSINE'>8DA</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2A5C is a [ | 2A5C is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A5C OCA]. | ||
==Reference== | ==Reference== | ||
Recognition of oxidatively modified bases within the biotin-binding site of avidin., Conners R, Hooley E, Clarke AR, Thomas S, Brady RL, J Mol Biol. 2006 Mar 17;357(1):263-74. Epub 2006 Jan 6. PMID:[http:// | Recognition of oxidatively modified bases within the biotin-binding site of avidin., Conners R, Hooley E, Clarke AR, Thomas S, Brady RL, J Mol Biol. 2006 Mar 17;357(1):263-74. Epub 2006 Jan 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16413579 16413579] | ||
[[Category: Gallus gallus]] | [[Category: Gallus gallus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: x-ray crystallography]] | [[Category: x-ray crystallography]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:45:37 2008'' | ||
Revision as of 13:45, 20 March 2008
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| 2a5c, resolution 2.500Å | |||||||||||||
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| Ligands: | NAG and 8DA | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine
Overview
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.
About this Structure
2A5C is a Single protein structure of sequence from Gallus gallus. Full crystallographic information is available from OCA.
Reference
Recognition of oxidatively modified bases within the biotin-binding site of avidin., Conners R, Hooley E, Clarke AR, Thomas S, Brady RL, J Mol Biol. 2006 Mar 17;357(1):263-74. Epub 2006 Jan 6. PMID:16413579
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