2of9: Difference between revisions
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==Crystal structure of apo AVR4 (D39A/C122S)== | ==Crystal structure of apo AVR4 (D39A/C122S)== | ||
<StructureSection load='2of9' size='340' side='right' caption='[[2of9]], [[Resolution|resolution]] 1.35Å' scene=''> | <StructureSection load='2of9' size='340' side='right'caption='[[2of9]], [[Resolution|resolution]] 1.35Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2of9]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2of9]] 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=2OF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OF9 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2of9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2of9 OCA], [https://pdbe.org/2of9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2of9 RCSB], [https://www.ebi.ac.uk/pdbsum/2of9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2of9 ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/AVR4_CHICK AVR4_CHICK] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/of/2of9_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/of/2of9_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2of9 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2of9" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Avidin|Avidin]] | *[[Avidin 3D structures|Avidin 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 34: | Line 37: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Gallus gallus]] | [[Category: Gallus gallus]] | ||
[[Category: Eisenberg-Domovich | [[Category: Large Structures]] | ||
[[Category: Hayouka | [[Category: Eisenberg-Domovich Y]] | ||
[[Category: Livnah | [[Category: Hayouka R]] | ||
[[Category: Livnah O]] | |||
Latest revision as of 08:23, 17 October 2024
Crystal structure of apo AVR4 (D39A/C122S)Crystal structure of apo AVR4 (D39A/C122S)
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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 AlsoReferences
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