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Avidin

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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]])'>
<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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__TOC__
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==Function==
[[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 />
[[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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* '''Hoefavidin''' from ''Hoeflea phototrophica''<br />
* '''Hoefavidin''' from ''Hoeflea phototrophica''<br />
* '''Shwanavidin''' from ''Shewanella dentrifica''<br />
* '''Shwanavidin''' from ''Shewanella dentrifica''<br />
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* '''Wilavidin''' from ''Gammaproteobacteria bacterium'' forms biotin-binding hexameters<br />
* '''AVR2''' and '''AVR4''' are avidin-related proteins.
* '''AVR2''' and '''AVR4''' are avidin-related proteins.
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].
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/5'>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/11'>two of those four units</scene>. <ref group="xtra">PMID:8506353</ref><ref group="xtra">PMID:8344421</ref>
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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>
{{Clear}}
{{Clear}}
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The binding affinity of biotin for the avidin <scene name='41/410356/Cv/10'>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 <scene name='41/410356/Cv/12'>biotin has bound a pocket in the avidin</scene>, it is almost imposible to remove it in a biologica system!
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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/13'>beta-barrel</scene>. Binding of biotin involves a highly stabilized network of polar and hydrophobic interactions.
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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.
The presence of additional hydrophobic and hydrophilic groups in the binding site of avidin may account for its higher affinity constant.
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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Unexpectedly, a residual N-acetylglucosamine moiety was detected in the deglycosylated avidin monomer. These <scene name='41/410356/Cv/14'>sugars</scene> appear along with the biotin but outside of the biotin binding pockets.
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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>.
See also:<br />
See also:<br />
* [[Molecular Playground/Streptavidin]]
* [[Molecular Playground/Streptavidin]]
* [[Streptavidin Binding Site]]
* [[Streptavidin Binding Site]]
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* [[Hila Cohen/Test Page]].
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* [[Hila Cohen/Test Page]]
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* [[Molecular Playground/Biotin binding avidin]]
==About this Structure==
==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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[[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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== 3D structures of Avidin ==
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[[Avidin 3D structures]]
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</StructureSection>
</StructureSection>
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== 3D structures of Avidin ==
 
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
 
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{{#tree:id=OrganizedByTopic|openlevels=0|
 
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*Avidin
 
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**[[3fdc]], [[2jgs]], [[2c4i]], [[1vyo]], [[1rav]], [[1ave]] – cAv – chicken<br />
 
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**[[2a5b]], [[2a5c]], [[2a8g]] – cAv+deoxyribose<br />
 
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**[[1nqn]], [[2cam]], [[4bcs]], [[4u46]], [[5lur]] – cAv (mutant)<br />
 
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**[[1ldo]], [[1ldq]], [[1lel]], [[1ij8]], [[1avd]], [[2avi]], [[3vgw]], [[3vhh]], [[3vhi]], [[3vhm]], [[4i60]], [[4jhq]], [[5hlm]], [[5iru]], [[5irw]], [[5myq]] – cAV + biotin derivative<br />
 
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**[[5chk]] – cAV+ HABA<br />
 
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**[[3szh]], [[3szi]] – SdAV – ''Shewanella denitrificans''<br />
 
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**[[3t2x]] – SdAV (mutant)<br />
 
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**[[3szj]] – SdAV + biotin<br />
 
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**[[3t2w]] – SdAV (mutant) + biotin
 
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* Streptavidin
 
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**[[2bc3]], [[2iza]], [[2izb]], [[2izc]], [[2izd]], [[2ize]], [[2rta]], [[2rtb]], [[2rtc]], [[3ry1]], [[4gd9]]. [[4gda]], [[4gjs]] - StrAv - ''Streptomyces avidinii''<br />
 
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**[[3mm0]], [[3pk2]], [[3rds]], [[3rdx]], [[3re5]], [[3re6]], [[4gjv]] - StrAv (mutant) <br />
 
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**[[1swa]], [[1swb]], [[1swc]], [[1ry1]] - StrAv core<br />
 
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**[[1swh]], [[1swj]], [[1swl]], [[1swo]], [[1swq]], [[1sws]], [[2y3e]], [[3t6l]] - StrAv core (mutant)<br />
 
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**[[4jnj]] – StrAv/rhizavidin<br />
 
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**[[4jo6]] – StrAv + SBP-TAG<br />
 
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*''Streptavidin binary complexes''
 
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**[[1rxh]] – StrAv (mutant)+ biotinyl p-nitroaniline<br />
 
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**[[1rxj]], [[1rxk]], [[1nqm]], [[1kff]], [[1kl4]], [[1luq]], [[1mm9]], [[1moy]], [[1n4j]], [[1n7y]], [[1n9y]], [[1nbx]], [[1swf]], [[1swu]], [[1kl3]], [[1kl5]] - StrAv (mutant) + strep-tag II peptide<br />
 
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**[[1rst]], [[1rsu]] - StrAv + strep-tag II peptide<br />
 
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**[[1df8]], [[1mep]], [[1n43]], [[1n9m]], [[1ndj]], [[1swg]], [[3rdm]], [[3rdo]], [[4ekv]] - StrAv (mutant)+biotin<br />
 
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**[[1nc9]], [[3rdq]], [[4dne]] - StrAv (mutant)+biotin derivative<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]], [[3ry2]] - StrAv core+biotin<br />
 
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**[[1swk]], [[1swn]], [[1swp]], [[1swr]], [[1swt]], [[3mg5]], [[2y3f]], [[3t6f]] - StrAv core (mutant) + biotin<br />
 
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**[[1stp]], [[2izf]], [[2izg]], [[2izh]], [[2izi]], [[2izj]], [[2rtd]], [[2rte]], [[2rtf]], [[2rtg]] - StrAv +biotin<br />
 
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**[[3rdu]] - StrAv (mutant) + PEG<br />
 
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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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* Rhizavidin
 
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**[[3ew1]] – RhiAv – ''Rhizobium etli''<br />
 
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**[[3ew2]] – RhiAV+biotin<br />
 
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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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* Bradavidin
 
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**[[4ggr]], [[4ggt]] – BjAv – ''Bradyrhizobium japonicum''<br />
 
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**[[4ggz]] – BjAv + biotin<br />
 
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*Hoefavidin
 
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**[[4z6j]] – HpAv – ''Hoeflea phototrophica''<br />
 
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**[[4z27]] – HpAv short <br />
 
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**[[4z28]] – HpAv short + biotin <br />
 
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**[[4z2p]], [[4z2v]], [[4z2o]] – HpAv short + peptide <br />
 
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*Shwanavidin
 
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**[[3szi]], [[3szh]] – SdAv – ''Shewanella dentrifica''<br />
 
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**[[3t2x]] – SdAv (mutant)<br />
 
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**[[3szj]] – SdAv + biotin<br />
 
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**[[3t2w]] – SdAv (mutant) + biotin<br />
 
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* Zebavidin
 
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**[[4bj8]] – Av – zebrafish<br />
 
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* Avidin-related protein AVR2
 
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**[[1wbi]] – cAVR2<br />
 
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*Avidin-related protein AVR4
 
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**[[2fhl]] – cAVR4+biotinyl p-nitroaniline<br />
 
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**[[2of9]], [[2ofa]], [[1y53]], [[3mm0]] - cAVR4 (mutant)<br />
 
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**[[2fhn]], [[2of8]], [[2ofb]] - cAVR4 (mutant)+biotinyl p-nitroaniline<br />
 
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**[[1y52]], [[1y55]] - cAVR4 (mutant)+biotin<br />
 
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**[[2mf6]] - cAVR4/Av (mutant)+biotin – NMR<br />
 
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}}
 
==Reference==
==Reference==

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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