3b35: Difference between revisions

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-{{Seed}}
-[[Image:3b35.png|left|200px]]
-<!--
+==Crystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus==
-The line below this paragraph, containing "STRUCTURE_3b35", creates the "Structure Box" on the page.
+<StructureSection load='3b35' size='340' side='right'caption='[[3b35]], [[Resolution|resolution]] 1.10&Aring;' 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'>[[3b35]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B35 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B35 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]] 1.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>
-{{STRUCTURE_3b35|  PDB=3b35  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b35 OCA], [https://pdbe.org/3b35 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b35 RCSB], [https://www.ebi.ac.uk/pdbsum/3b35 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b35 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMPX_VIBPR AMPX_VIBPR]
+== 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/b3/3b35_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=3b35 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The 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.
-===Crystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus===
+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<ref>PMID:18576673</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3b35" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18576673}}, adds the Publication Abstract to the page
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18576673 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18576673}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-B35 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B35 OCA].
-==Reference==
-<ref group="xtra">PMID:18576673</ref><references group="xtra"/>
-[[Category: Bacterial leucyl aminopeptidase]]
 [[Category: Vibrio proteolyticus]]
-[[Category: Ataie, N J.]]
+[[Category: Ataie NJ]]
-[[Category: Hoang, Q Q.]]
+[[Category: Hoang QQ]]
-[[Category: Petsko, G A.]]
+[[Category: Petsko GA]]
-[[Category: Ringe, D.]]
+[[Category: Ringe D]]
-[[Category: Alpha beta]]
-[[Category: Aminopeptidase]]
-[[Category: Hydrolase]]
-[[Category: Metal-binding]]
-[[Category: Protease]]
-[[Category: Secreted]]
-[[Category: Zinc]]
-[[Category: Zymogen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:17:51 2009''