Avidin

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[[Image:1ave1.png|left|200px|thumb|Crystal Structure of Chicken Apo-Avidin, [[1ave]]]]
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<StructureSection load='2avi' size='350' side='right' scene='41/410356/Cv/4' caption='The avidin tetramer complex with biotin (PDB code [[2avi]])'>
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{{STRUCTURE_1ave| PDB=1ave | SIZE=300| SCENE=Avidin/Cv/3 |right|CAPTION=Chicken Apo-Avidin, [[1ave]] }}
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__TOC__
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'''3D Structure of Avidin'''
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==Function==
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[[Avidin]] '''(Av)''' is a protein found in egg white which binds biotin (vitamin B7) with high affinity. This property makes it a powerful tool in various protein pull-down assays. Similar proteins are strepavidin (StrAv) from the bacterium ''Streptomyces avidinii'', Rhizavidin (RhiAv) from ''Rhizobium etli'', Xenavidin from frog, and the avidin-related proteins AVR2 and AVR4. The N-acetylglucosamine sugars are shown as space filling objects in the image on the left.
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[[Avidin]] '''(Av)''' is a protein found in egg white which binds biotin (vitamin B7) with high affinity. This property makes it a powerful tool in various protein pull-down assays. Similar proteins are:<br />
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* '''Streptavidin''' (StrAv) from the bacterium ''Streptomyces avidinii''<br />
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* '''Rhizavidin''' (RhiAv) from ''Rhizobium etli''<br />
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* '''Xenavidin''' from frog<br />
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* '''Zebavidin''' from zebrafish<br />
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* '''Tamavidin''' from fungi<br />
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* '''Bradavidin''' from ''Bradyrhizobium japonicum''<br />
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* '''Hoefavidin''' from ''Hoeflea phototrophica''<br />
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* '''Shwanavidin''' from ''Shewanella dentrifica''<br />
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* '''Wilavidin''' from ''Gammaproteobacteria bacterium'' forms biotin-binding hexameters<br />
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* '''AVR2''' and '''AVR4''' are avidin-related proteins.
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Avidin is one of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
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<scene name='41/410356/Cv/15'>Avidin is a tetrameric protein</scene> what in different words means that if we could, we would see a protein with four regions that look identical one to the other. However, to isolate the four regions as a whole in order to show the protein three dimensional structure has been quite diffucult so far and we just can see the three dimensional structure for <scene name='41/410356/Cv/16'>two of those four units</scene>. <ref group="xtra">PMID:8506353</ref><ref group="xtra">PMID:8344421</ref>
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{{TOC limit|limit=2}}
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{{Clear}}
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== Avidin ==
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The binding affinity of biotin for the avidin <scene name='41/410356/Cv/17'>receptors</scene> is very hight or in other words, the strength of the interations between the biotin and the avidin receptors is so strong that washing the biotin-avidin complex is not enough to remove the ligand from its pocket. This is not even possible by adding more biotin molecules to the system avidin-biotin. Once a biotin has bound a pocket in the avidin, it is almost imposible to remove it in a biological system!
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Each monomer is an eight-stranded antiparallel <scene name='41/410356/Cv/18'>beta-barrel</scene>. Binding of biotin involves a highly stabilized network of polar and hydrophobic interactions.
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[[3fdc]], [[2jgs]], [[2c4i]], [[1vyo]], [[1rav]], [[1ave]] – cAv – chicken<br />
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The presence of additional hydrophobic and hydrophilic groups in the binding site of avidin may account for its higher affinity constant.
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[[2a5b]], [[2a5c]], [[2a8g]] – cAv+deoxyribose<br />
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[[1nqn]], [[2cam]] – cAv (mutant)<br />
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[[1ldo]], [[1ldq]], [[1lel]], [[1ij8]], [[1avd]], [[2avi]] – cAV + biotin derivative<br />
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Unexpectedly, a residual N-acetylglucosamine moiety was detected in the deglycosylated avidin monomer. These <scene name='41/410356/Cv/19'>sugars</scene> appear along with the biotin but outside of the biotin binding pockets.
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*<scene name='41/410356/Cv/20'>Biotin has bound a pocket in the avidin</scene>.
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See also:<br />
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* [[Molecular Playground/Streptavidin]]
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* [[Streptavidin Binding Site]]
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* [[Hila Cohen/Test Page]]
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* [[Molecular Playground/Biotin binding avidin]]
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== Strepavidin ==
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==About this Structure==
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[[2avi]] is a 2 chains structure of sequences 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=2AVI OCA].
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[[2bc3]], [[2iza]], [[2izb]], [[2izc]], [[2izd]], [[2ize]], [[2rta]], [[2rtb]], [[2rtc]] - StrAv - ''Streptomyces avidinii''<br />
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== 3D structures of Avidin ==
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[[1rxh]] – StrAv (mutant)+ biotinyl p-nitroaniline <br />
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[[Avidin 3D structures]]
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[[1rxj]], [[1rxk]], [[1nqm]], [[1kff]], [[1kl4]], [[1luq]], [[1mm9]], [[1moy]], [[1n4j]], [[1n7y]], [[1n9y]], [[1nbx]], [[1swf]], [[1swu]], [[3mm0]] - StrAv (mutant) <br />
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[[1kl3]], [[1kl5]] - StrAv (mutant) + strep-tag II peptide<br />
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</StructureSection>
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[[1rst]], [[1rsu]] - StrAv + strep-tag II peptide<br />
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[[1df8]], [[1mep]], [[1n43]], [[1n9m]], [[1ndj]], [[1swg]] - StrAv (mutant)+biotin<br />
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[[1nc9]] - StrAv (mutant)+iminobiotin<br />
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[[2izl]], [[2rtl]], [[2rtm]], [[2rtn]], [[2rto]], [[2rtp]], [[2rtq]], [[2rtr]] - StrAv +iminobiotin<br />
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[[1mk5]], [[1swd]], [[1swe]], [[2f01]], [[2gh7]] - StrAv core+biotin<br />
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[[1swa]], [[1swb]], [[1swc]] - StrAv core<br />
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[[1swh]], [[1swj]], [[1swl]], [[1swo]], [[1swq]], [[1sws]], [[2y3e]] - StrAv core (mutant)<br />
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[[1swk]], [[1swn]], [[1swp]], [[1swr]], [[1swt]], [[3mg5]], [[2y3f]] - StrAv core (mutant) + biotin<br />
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[[1stp]], [[2izf]], [[2izg]], [[2izh]], [[2izi]], [[2izj]], [[2rtd]], [[2rte]], [[2rtf]], [[2rtg]] - StrAv +biotin
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[[1hqq]], [[1hxl]] – StrAv + MP-2 (mutant)<br />
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[[1hy2]] - StrAv + MP-1 <br />
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[[1hxz]] - StrAv + MP-2<br />
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[[1pts]], [[1sld]], [[1sle]], [[1slg]], [[1str]], [[1sts]], [[1vwa]], [[1vwb]], [[1vwc]], [[1vwd]], [[1vwe]], [[1vwf]], [[1vwg]], [[1vwh]], [[1vwi]], [[1vwj]], [[1vwk]], [[1vwl]], [[1vwm]], [[1vwn]], [[1vwo]], [[1vwp]], [[1vwq]], [[1vwr]], [[2g5l]] - StrAv + peptide<br />
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[[1slf]] - StrAv + SO4<br />
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[[1sre]], [[1srf]], [[1srg]], [[1srh]], [[1sri]], [[1srj]] - StrAv + benzoic acid ligands<br />
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[[1lcv]], [[1lcw]], [[1lcz]], [[1i9h]] – StrAv+biotin derivative<br />
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[[2izk]], [[2rth]], [[2rti]], [[2rtj]], [[2rtk]] – StrAV+glycouril<br />
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[[2qcb]], [[2wpu]] – StrAv+Ru ligand
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==Reference==
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== Rhizavidin ==
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<references group="xtra"/>
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[[Category: Gallus gallus]]
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[[Category: Livnah, O.]]
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[[3ew1]] – RhiAv – ''Rhizobium etli''<br />
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[[Category: Sussman, J.]]
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[[3ew2]] – RhiAV+biotin<br />
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[[Category: Biotin binding protein]]
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== Xenavidin ==
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[[2uz2]], [[2uyw]] – XenAv – frog<br />
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== Tamavidin ==
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[[2zsc]] – TanAv – Tamogitake mushroom
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== AVR2 ==
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[[1wbi]] – cAVR2<br />
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== AVR4 ==
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[[2fhl]] – cAVR4+biotinyl p-nitroaniline<br />
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[[2of9]], [[2ofa]], [[1y53]] - cAVR4 (mutant)<br />
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[[2fhn]], [[2of8]] - cAVR4 (mutant)+biotinyl p-nitroaniline<br />
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[[1y52]], [[1y55]] - cAVR4 (mutant)+biotin<br />
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[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

The avidin tetramer complex with biotin (PDB code 2avi)

Drag the structure with the mouse to rotate

Reference

  • Livnah O, Bayer EA, Wilchek M, Sussman JL. Three-dimensional structures of avidin and the avidin-biotin complex. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5076-80. PMID:8506353
  • Livnah O, Bayer EA, Wilchek M, Sussman JL. The structure of the complex between avidin and the dye, 2-(4'-hydroxyazobenzene) benzoic acid (HABA). FEBS Lett. 1993 Aug 9;328(1-2):165-8. PMID:8344421
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