3b3t: Difference between revisions
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==Crystal structure of the D118N mutant of the aminopeptidase from Vibrio proteolyticus== | ==Crystal structure of the D118N mutant of the aminopeptidase from Vibrio proteolyticus== | ||
<StructureSection load='3b3t' size='340' side='right' caption='[[3b3t]], [[Resolution|resolution]] 1.17Å' scene=''> | <StructureSection load='3b3t' size='340' side='right'caption='[[3b3t]], [[Resolution|resolution]] 1.17Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3b3t]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3b3t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"aeromonas_proteolytica"_merkel_et_al._1964 "aeromonas proteolytica" merkel et al. 1964]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B3T FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ILE:ISOLEUCINE'>ILE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ILE:ISOLEUCINE'>ILE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b35|3b35]], [[3b3c|3b3c]], [[3b3s|3b3s]], [[3b3v|3b3v]], [[3b3w|3b3w]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3b35|3b35]], [[3b3c|3b3c]], [[3b3s|3b3s]], [[3b3v|3b3v]], [[3b3w|3b3w]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AAP ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AAP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 "Aeromonas proteolytica" Merkel et al. 1964])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3t OCA], [https://pdbe.org/3b3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b3t RCSB], [https://www.ebi.ac.uk/pdbsum/3b3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3t ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/3b3t_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/3b3t_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 3b3t" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3b3t" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Aeromonas proteolytica merkel et al. 1964]] | [[Category: Aeromonas proteolytica merkel et al. 1964]] | ||
[[Category: Bacterial leucyl aminopeptidase]] | [[Category: Bacterial leucyl aminopeptidase]] | ||
[[Category: Large Structures]] | |||
[[Category: Ataie, N J]] | [[Category: Ataie, N J]] | ||
[[Category: Hoang, Q Q]] | [[Category: Hoang, Q Q]] | ||
Revision as of 21:53, 20 October 2021
Crystal structure of the D118N mutant of the aminopeptidase from Vibrio proteolyticusCrystal structure of the D118N mutant of the aminopeptidase from Vibrio proteolyticus
Structural highlights
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 PubMedThe chemical properties of zinc make it an ideal metal to study the role of coordination strain in enzymatic rate enhancement. The zinc ion and the protein residues that are bound directly to the zinc ion represent a functional charge/dipole complex, and polarization of this complex, which translates to coordination distortion, may tune electrophilicity, and hence, reactivity. Conserved protein residues outside of the charge/dipole complex, such as second-shell residues, may play a role in supporting the electronic strain produced as a consequence of functional polarization. To test the correlation between charge/dipole polarity and ligand binding affinity, structure-function studies were carried out on the dizinc aminopeptidase from Vibrio proteolyticus. Alanine substitutions of S228 and M180 resulted in catalytically diminished enzymes whose crystal structures show very little change in the positions of the metal ions and the protein residues. However, more detailed inspections of the crystal structures show small positional changes that account for differences in the zinc ion coordination geometry. Measurements of the binding affinity of leucine phosphonic acid, a transition state analogue, and leucine, a product, show a correlation between coordination geometry and ligand binding affinity. These results suggest that the coordination number and polarity may tune the electrophilicity of zinc. This may have provided the evolving enzyme with the ability to discriminate between reaction coordinate species. Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus.,Ataie NJ, Hoang QQ, Zahniser MP, Tu Y, Milne A, Petsko GA, Ringe D Biochemistry. 2008 Jul 22;47(29):7673-83. Epub 2008 Jun 25. PMID:18576673[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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