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| [[Image:1ave1.png|left|200px|thumb|Crystal Structure of Chicken Apo-Avidin, [[1ave]]]]
| | <StructureSection load='2avi' size='350' side='right' scene='41/410356/Cv/4' caption='The avidin tetramer complex with biotin (PDB code [[2avi]])'> |
| {{STRUCTURE_1ave| PDB=1ave | SIZE=300| SCENE=Avidin/Cv/3 |right|CAPTION=Chicken Apo-Avidin, [[1ave]] }}
| | __TOC__ |
| | ==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:<br /> |
| | | * '''Streptavidin''' (StrAv) from the bacterium ''Streptomyces avidinii''<br /> |
| | | * '''Rhizavidin''' (RhiAv) from ''Rhizobium etli''<br /> |
| | | * '''Xenavidin''' from frog<br /> |
| | | * '''Zebavidin''' from zebrafish<br /> |
| | | * '''Tamavidin''' from fungi<br /> |
| | | * '''Bradavidin''' from ''Bradyrhizobium japonicum''<br /> |
| | | * '''Hoefavidin''' from ''Hoeflea phototrophica''<br /> |
| | | * '''Shwanavidin''' from ''Shewanella dentrifica''<br /> |
| | | * '''Wilavidin''' from ''Gammaproteobacteria bacterium'' forms biotin-binding hexameters<br /> |
| | | * '''AVR2''' and '''AVR4''' are avidin-related proteins. |
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| '''3D Structure of Avidin'''
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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 streptavidin (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 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/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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| Avidin is a tetrameric protein 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 two of those four units. <ref group="xtra">PMID:8506353</ref><ref group="xtra">PMID:8344421</ref>
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| The binding affinity of biotin for the avidin <scene name='Sandbox-test/Biotin_binding_avidin/1'>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 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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| <applet load='2avi' size='300' frame='true' align='right' caption='Two monomers of the tetramer Avidin' /> Each monomer is an eight-stranded antiparallel <scene name='Sandbox-test/Avidin_b-barrels/1'>beta-barrel</scene>. Binding of biotin involves a highly stabilized network of polar and hydrophobic interactions.
| | 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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| 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='Sandbox-test/Ligands/1'>sugars</scene> appear along with the biotin but outside of the biotin binding pockets. | | 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. |
| | | *<scene name='41/410356/Cv/20'>Biotin has bound a pocket in the avidin</scene>. |
| {{TOC limit|limit=2}}
| | See also:<br /> |
| | * [[Molecular Playground/Streptavidin]] |
| | * [[Streptavidin Binding Site]] |
| | * [[Hila Cohen/Test Page]] |
| | * [[Molecular Playground/Biotin binding avidin]] |
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| ==About this Structure== | | ==About this Structure== |
| 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].
| | [[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 == | | == 3D structures of Avidin == |
| | | [[Avidin 3D structures]] |
| ''Update November 2011''
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| | | </StructureSection> |
| [[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]] – cAv (mutant)<br />
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| [[1ldo]], [[1ldq]], [[1lel]], [[1ij8]], [[1avd]], [[2avi]] – cAV + biotin derivative<br />
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| == Streptavidin ==
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| [[2bc3]], [[2iza]], [[2izb]], [[2izc]], [[2izd]], [[2ize]], [[2rta]], [[2rtb]], [[2rtc]], [[3ry1]] - StrAv - ''Streptomyces avidinii''<br />
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| [[3mm0]], [[3pk2]], [[3rds]], [[3rdx]], [[3re5]], [[3re6]] - 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]] - StrAv core (mutant)<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]],
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| [[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]] - StrAv (mutant)+biotin<br />
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| [[1nc9]], [[3rdq]] - 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]] - 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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| == 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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| ==Reference== | | ==Reference== |