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2a5b

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(New page: 200px<br /><applet load="2a5b" size="450" color="white" frame="true" align="right" spinBox="true" caption="2a5b, resolution 2.49&Aring;" /> '''Avidin complexed wit...)
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[[Image:2a5b.gif|left|200px]]<br /><applet load="2a5b" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2a5b, resolution 2.49&Aring;" />
 
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'''Avidin complexed with 8-oxodeoxyguanosine'''<br />
 
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==Overview==
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==Avidin complexed with 8-oxodeoxyguanosine==
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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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<StructureSection load='2a5b' size='340' side='right'caption='[[2a5b]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2a5b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A5B FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.49&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8HG:2-DEOXY-8-OXOGUANOSINE'>8HG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2a5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a5b OCA], [https://pdbe.org/2a5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a5b RCSB], [https://www.ebi.ac.uk/pdbsum/2a5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a5b ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/AVID_CHICK AVID_CHICK] The biological function of avidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of avidin).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a5/2a5b_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2a5b ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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==About this Structure==
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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<ref>PMID:16413579</ref>
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2A5B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with NAG and 8HG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2A5B OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=16413579 16413579]
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</div>
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[[Category: Gallus gallus]]
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<div class="pdbe-citations 2a5b" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Brady, R.L.]]
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[[Category: Conners, R.]]
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[[Category: Hooley, E.]]
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[[Category: Thomas, S.]]
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[[Category: 8HG]]
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[[Category: NAG]]
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[[Category: 8-oxodeoxyguanosine]]
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[[Category: avidin]]
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[[Category: damaged dna]]
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[[Category: x-ray crystallography]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:55:31 2007''
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==See Also==
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*[[Avidin 3D structures|Avidin 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Gallus gallus]]
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[[Category: Large Structures]]
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[[Category: Brady RL]]
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[[Category: Conners R]]
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[[Category: Hooley E]]
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[[Category: Thomas S]]

Current revision

Avidin complexed with 8-oxodeoxyguanosine

PDB ID 2a5b

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