3bh3: Difference between revisions

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-{{Seed}}
-[[Image:3bh3.png|left|200px]]
-<!--
+==Crystal structure of acetoacetate decarboxylase from Chromobacterium violaceum in complex with acetyl acetone Schiff base intermediate==
-The line below this paragraph, containing "STRUCTURE_3bh3", creates the "Structure Box" on the page.
+<StructureSection load='3bh3' size='340' side='right'caption='[[3bh3]], [[Resolution|resolution]] 2.10&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'>[[3bh3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chromobacterium_violaceum_ATCC_12472 Chromobacterium violaceum ATCC 12472]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BH3 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PNH:PENTAN-2-ONE'>PNH</scene></td></tr>
-{{STRUCTURE_3bh3|  PDB=3bh3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bh3 OCA], [https://pdbe.org/3bh3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bh3 RCSB], [https://www.ebi.ac.uk/pdbsum/3bh3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bh3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADC_CHRVO ADC_CHRVO] Catalyzes the conversion of acetoacetate to acetone and carbon dioxide (By similarity).
+== 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/bh/3bh3_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=3bh3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Acetoacetate decarboxylase (AADase) has long been cited as the prototypical example of the marked shifts in the pK(a) values of ionizable groups that can occur in an enzyme active site. In 1966, it was hypothesized that in AADase the origin of the large pK(a) perturbation (-4.5 log units) observed in the nucleophilic Lys 115 results from the proximity of Lys 116, marking the first proposal of microenvironment effects in enzymology. The electrostatic perturbation hypothesis has been demonstrated in a number of enzymes, but never for the enzyme that inspired its conception, owing to the lack of a three-dimensional structure. Here we present the X-ray crystal structures of AADase and of the enamine adduct with the substrate analogue 2,4-pentanedione. Surprisingly, the shift of the pK(a) of Lys 115 is not due to the proximity of Lys 116, the side chain of which is oriented away from the active site. Instead, Lys 116 participates in the structural anchoring of Lys 115 in a long, hydrophobic funnel provided by the novel fold of the enzyme. Thus, AADase perturbs the pK(a) of the nucleophile by means of a desolvation effect by placement of the side chain into the protein core while enforcing the proximity of polar residues, which facilitate decarboxylation through electrostatic and steric effects.
-===Crystal structure of acetoacetate decarboxylase from Chromobacterium violaceum in complex with acetyl acetone Schiff base intermediate===
+The origin of the electrostatic perturbation in acetoacetate decarboxylase.,Ho MC, Menetret JF, Tsuruta H, Allen KN Nature. 2009 May 21;459(7245):393-7. PMID:19458715<ref>PMID:19458715</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19458715}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3bh3" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19458715 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19458715}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Chromobacterium violaceum ATCC 12472]]
-BH3 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Chromobacterium_violaceum_atcc_12472 Chromobacterium violaceum atcc 12472]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BH3 OCA].
+[[Category: Large Structures]]
+[[Category: Allen KN]]
-==Reference==
+[[Category: Ho M]]
-<ref group="xtra">PMID:19458715</ref><references group="xtra"/>
-[[Category: Acetoacetate decarboxylase]]
-[[Category: Chromobacterium violaceum atcc 12472]]
-[[Category: Allen, K N.]]
-[[Category: Ho, M.]]
-[[Category: Acetoacetate decarboxylase]]
-[[Category: Lyase]]
-[[Category: Schiff base intermediate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun  3 10:11:05 2009''