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| - | [[Image:2of8.jpg|left|200px]] | |
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| - | <!-- | + | ==Crystal structure of AVR4 (D39A/C122S)-BNA complex== |
| - | The line below this paragraph, containing "STRUCTURE_2of8", creates the "Structure Box" on the page.
| + | <StructureSection load='2of8' size='340' side='right'caption='[[2of8]], [[Resolution|resolution]] 1.05Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet) | + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2of8]] 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=2OF8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OF8 FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display. | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.05Å</td></tr> |
| - | -->
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNI:5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-NITRO-PHENYL)-AMIDE'>BNI</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr> |
| - | {{STRUCTURE_2of8| PDB=2of8 | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2of8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2of8 OCA], [https://pdbe.org/2of8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2of8 RCSB], [https://www.ebi.ac.uk/pdbsum/2of8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2of8 ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/AVR4_CHICK AVR4_CHICK] |
| | + | == 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/of/2of8_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2of8 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The homotetrameric and biotin-binding properties of avidin and streptavidin have been exploited for a myriad of biotechnological applications and theoretical studies. Among the few differences between the two proteins is the capacity of avidin to hydrolyze biotinyl p-nitrophenyl ester (BNP), as opposed to streptavidin, which fully protects the same pseudosubstrate from hydrolysis. Combined mutagenesis and X-ray analysis have been used to attempt to understand this diametric difference in activities. It was found that a charged residue and one of the loops (L3,4) are together responsible for this difference. Recently, the avidin-related analogue AVR4 was found to have an even more pronounced BNP-hydrolysis activity than avidin. Again, the combination of charged residue(s) (Asp39 and/or Arg112) and the rigid conformation of the L3,4 loop was suggested to be responsible for the observed hydrolysis reaction. However, replacement of the latter charged residues in AVR4 resulted in only a modest reduction in hydrolytic activity at most, whereas replacement of the L3,4 loop of avidin with the rigid loop of AVR4 caused a dramatic increase in the activity of avidin. These results clearly demonstrate that the main feature responsible for the observed differences in rates of hydrolysis among the avidins is the conformational status of the L3,4 loop, which imposes conformational constraints on the pseudosubstrate, thereby rendering it susceptible to nucleophilic attack by solvent. In this context, the hydrolytic properties of the avidins reflect enzyme catalysis, in that subtleties in substrate binding are the determining features of catalytic efficiency. |
| | | | |
| - | '''Crystal structure of AVR4 (D39A/C122S)-BNA complex'''
| + | Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester.,Hayouka R, Eisenberg-Domovich Y, Hytonen VP, Maatta JA, Nordlund HR, Kulomaa MS, Wilchek M, Bayer EA, Livnah O Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):302-8. Epub 2008, Feb 20. PMID:18323625<ref>PMID:18323625</ref> |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | The homotetrameric and biotin-binding properties of avidin and streptavidin have been exploited for a myriad of biotechnological applications and theoretical studies. Among the few differences between the two proteins is the capacity of avidin to hydrolyze biotinyl p-nitrophenyl ester (BNP), as opposed to streptavidin, which fully protects the same pseudosubstrate from hydrolysis. Combined mutagenesis and X-ray analysis have been used to attempt to understand this diametric difference in activities. It was found that a charged residue and one of the loops (L3,4) are together responsible for this difference. Recently, the avidin-related analogue AVR4 was found to have an even more pronounced BNP-hydrolysis activity than avidin. Again, the combination of charged residue(s) (Asp39 and/or Arg112) and the rigid conformation of the L3,4 loop was suggested to be responsible for the observed hydrolysis reaction. However, replacement of the latter charged residues in AVR4 resulted in only a modest reduction in hydrolytic activity at most, whereas replacement of the L3,4 loop of avidin with the rigid loop of AVR4 caused a dramatic increase in the activity of avidin. These results clearly demonstrate that the main feature responsible for the observed differences in rates of hydrolysis among the avidins is the conformational status of the L3,4 loop, which imposes conformational constraints on the pseudosubstrate, thereby rendering it susceptible to nucleophilic attack by solvent. In this context, the hydrolytic properties of the avidins reflect enzyme catalysis, in that subtleties in substrate binding are the determining features of catalytic efficiency.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 2OF8 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=2OF8 OCA].
| + | </div> |
| | + | <div class="pdbe-citations 2of8" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester., Hayouka R, Eisenberg-Domovich Y, Hytonen VP, Maatta JA, Nordlund HR, Kulomaa MS, Wilchek M, Bayer EA, Livnah O, Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):302-8. Epub 2008, Feb 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18323625 18323625]
| + | *[[Avidin 3D structures|Avidin 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Gallus gallus]] | | [[Category: Gallus gallus]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Eisenberg-Domovich, Y.]] | + | [[Category: Eisenberg-Domovich Y]] |
| - | [[Category: Hayouka, R.]] | + | [[Category: Hayouka R]] |
| - | [[Category: Livnah, O.]] | + | [[Category: Livnah O]] |
| - | [[Category: Avidin]]
| + | |
| - | [[Category: Avr4]]
| + | |
| - | [[Category: High affinity]]
| + | |
| - | [[Category: Ligand binding protein]]
| + | |
| - | [[Category: Pseudo-catalysis]]
| + | |
| - | [[Category: Streptavidin]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:25:34 2008''
| + | |
| Structural highlights
Function
AVR4_CHICK
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
The homotetrameric and biotin-binding properties of avidin and streptavidin have been exploited for a myriad of biotechnological applications and theoretical studies. Among the few differences between the two proteins is the capacity of avidin to hydrolyze biotinyl p-nitrophenyl ester (BNP), as opposed to streptavidin, which fully protects the same pseudosubstrate from hydrolysis. Combined mutagenesis and X-ray analysis have been used to attempt to understand this diametric difference in activities. It was found that a charged residue and one of the loops (L3,4) are together responsible for this difference. Recently, the avidin-related analogue AVR4 was found to have an even more pronounced BNP-hydrolysis activity than avidin. Again, the combination of charged residue(s) (Asp39 and/or Arg112) and the rigid conformation of the L3,4 loop was suggested to be responsible for the observed hydrolysis reaction. However, replacement of the latter charged residues in AVR4 resulted in only a modest reduction in hydrolytic activity at most, whereas replacement of the L3,4 loop of avidin with the rigid loop of AVR4 caused a dramatic increase in the activity of avidin. These results clearly demonstrate that the main feature responsible for the observed differences in rates of hydrolysis among the avidins is the conformational status of the L3,4 loop, which imposes conformational constraints on the pseudosubstrate, thereby rendering it susceptible to nucleophilic attack by solvent. In this context, the hydrolytic properties of the avidins reflect enzyme catalysis, in that subtleties in substrate binding are the determining features of catalytic efficiency.
Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester.,Hayouka R, Eisenberg-Domovich Y, Hytonen VP, Maatta JA, Nordlund HR, Kulomaa MS, Wilchek M, Bayer EA, Livnah O Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):302-8. Epub 2008, Feb 20. PMID:18323625[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hayouka R, Eisenberg-Domovich Y, Hytonen VP, Maatta JA, Nordlund HR, Kulomaa MS, Wilchek M, Bayer EA, Livnah O. Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester. Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):302-8. Epub 2008, Feb 20. PMID:18323625 doi:10.1107/S0907444907067844
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