This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2a8g

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 09:08, 11 September 2015

Structure of Avidin in complex with the ligand deoxyguanosine

Structural highlights

2a8g is a 2 chain structure with sequence from Chick. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Conners R, Hooley E, Clarke AR, Thomas S, Brady RL. Recognition of oxidatively modified bases within the biotin-binding site of avidin. J Mol Biol. 2006 Mar 17;357(1):263-74. Epub 2006 Jan 6. PMID:16413579 doi:10.1016/j.jmb.2005.12.054

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2a8g"

@@ Line 2: / Line 2: @@
 <StructureSection load='2a8g' size='340' side='right' caption='[[2a8g]], [[Resolution|resolution]] 1.99&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2a8g]] is a 2 chain structure with 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=2A8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2a8g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8G FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a8g RCSB], [http://www.ebi.ac.uk/pdbsum/2a8g PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8g OCA], [http://pdbe.org/2a8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a8g RCSB], [http://www.ebi.ac.uk/pdbsum/2a8g PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 26: / Line 26: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2a8g" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 33: / Line 34: @@
 __TOC__
 </StructureSection>
-[[Category: Gallus gallus]]
+[[Category: Chick]]
 [[Category: Brady, R L]]
 [[Category: Conners, R]]

2a8g

From Proteopedia

Revision as of 09:08, 11 September 2015

Structure of Avidin in complex with the ligand deoxyguanosine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox