6jst
From Proteopedia
(Difference between revisions)
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<StructureSection load='6jst' size='340' side='right'caption='[[6jst]], [[Resolution|resolution]] 1.73Å' scene=''> | <StructureSection load='6jst' size='340' side='right'caption='[[6jst]], [[Resolution|resolution]] 1.73Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6jst]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JST OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JST FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6jst]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Geoka Geoka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JST OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JST FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LAE:3-OXO-OCTANOIC+ACID+(2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE'>LAE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LAE:3-OXO-OCTANOIC+ACID+(2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE'>LAE</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GK1506 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jst FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jst OCA], [http://pdbe.org/6jst PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jst RCSB], [http://www.ebi.ac.uk/pdbsum/6jst PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jst ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jst FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jst OCA], [http://pdbe.org/6jst PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jst RCSB], [http://www.ebi.ac.uk/pdbsum/6jst PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jst ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | In this work, we present a generalizable directed computational evolution protocol to effectively reduce the sequence space to be explored in rational enzyme design. The protocol involves in silico mutation modeling and substrate docking to rapidly identify mutagenesis hotspots that may enhance an enzyme's substrate binding and overall catalysis. By applying this protocol to a quorum-quenching Geobacillus kaustophilus lactonase, GKL, we generated 1,881 single mutants and docked high-energy intermediates of nine acyl homoserine lactones onto them. We found that Phe28 and Tyr99 were two hotspots that produced most of the predicted top 20 mutants. Of the 180 enzyme-substrate combinations (top 20 mutants x 9 substrates), 51 (28%) exhibited enhanced substrate binding and 22 (12%) had better overall activity when compared with wild-type GKL. X-ray crystallographic studies of Y99C and Y99P provided rationalized explanations for the enhancement in enzyme function and corroborated the utility of the protocol. | ||
| + | |||
| + | Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily.,Go MK, Zhao LN, Xue B, Supekar S, Robinson RC, Fan H, Yew WS Structure. 2020 Apr 6. pii: S0969-2126(20)30093-9. doi:, 10.1016/j.str.2020.03.011. PMID:32320671<ref>PMID:32320671</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6jst" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Geoka]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Xue, B]] | [[Category: Xue, B]] | ||
Revision as of 06:24, 6 May 2020
Structure of Geobacillus kaustophilus lactonase, Y99P/D266N double mutant with bound 3-oxo-C8-HSL
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