3bh3: Difference between revisions
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<StructureSection load='3bh3' size='340' side='right' caption='[[3bh3]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='3bh3' size='340' side='right' caption='[[3bh3]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3bh3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3bh3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chrvo Chrvo]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BH3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PNH:PENTAN-2-ONE'>PNH</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PNH:PENTAN-2-ONE'>PNH</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bgt|3bgt]], [[3bh2|3bh2]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bgt|3bgt]], [[3bh2|3bh2]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adc, CV_3520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243365 | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adc, CV_3520 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243365 CHRVO])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetoacetate_decarboxylase Acetoacetate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.4 4.1.1.4] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetoacetate_decarboxylase Acetoacetate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.4 4.1.1.4] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bh3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bh3 RCSB], [http://www.ebi.ac.uk/pdbsum/3bh3 PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bh3 OCA], [http://pdbe.org/3bh3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bh3 RCSB], [http://www.ebi.ac.uk/pdbsum/3bh3 PDBsum]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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<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=3bh3 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 3bh3" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Acetoacetate decarboxylase]] | [[Category: Acetoacetate decarboxylase]] | ||
[[Category: | [[Category: Chrvo]] | ||
[[Category: Allen, K N]] | [[Category: Allen, K N]] | ||
[[Category: Ho, M]] | [[Category: Ho, M]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
[[Category: Schiff base intermediate]] | [[Category: Schiff base intermediate]] | ||
Revision as of 21:22, 8 February 2016
Crystal structure of acetoacetate decarboxylase from Chromobacterium violaceum in complex with acetyl acetone Schiff base intermediateCrystal structure of acetoacetate decarboxylase from Chromobacterium violaceum in complex with acetyl acetone Schiff base intermediate
Structural highlights
Function[ADC_CHRVO] Catalyzes the conversion of acetoacetate to acetone and carbon dioxide (By similarity). 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 PubMedAcetoacetate 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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