2a5c: Difference between revisions

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-[[Image:2a5c.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2a5c", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_2a5c|  PDB=2a5c  |  SCENE=  }}
-'''Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine'''
+==Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine==
+<StructureSection load='2a5c' size='340' side='right'caption='[[2a5c]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2a5c]] 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=2A5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A5C FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8DA:8-OXODEOXYADENOSINE'>8DA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2a5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a5c OCA], [https://pdbe.org/2a5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a5c RCSB], [https://www.ebi.ac.uk/pdbsum/2a5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a5c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a5/2a5c_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2a5c ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-==Overview==
+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>
-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==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-A5C 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].
+</div>
+<div class="pdbe-citations 2a5c" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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]
+*[[Avidin 3D structures|Avidin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Brady, R L.]]
+[[Category: Brady RL]]
-[[Category: Conners, R.]]
+[[Category: Conners R]]
-[[Category: Hooley, E.]]
+[[Category: Hooley E]]
-[[Category: Thomas, S.]]
+[[Category: Thomas S]]
-[[Category: 8-oxodeoxyadenosine]]
-[[Category: Avidin]]
-[[Category: Damaged dna]]
-[[Category: X-ray crystallography]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 18:37:30 2008''