8sfd: Difference between revisions
New page: '''Unreleased structure''' The entry 8sfd is ON HOLD Authors: Jacquet, P., Billot, R., Shimon, A., Hoekstra, N., Bergonzi, C., Jenks, A., Daude, D., Elias, M.H. Description: Crystal st... |
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The | ==Crystal structure of the engineered SsoPox variant IVB10== | ||
<StructureSection load='8sfd' size='340' side='right'caption='[[8sfd]], [[Resolution|resolution]] 1.50Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8sfd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8SFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8SFD FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8sfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8sfd OCA], [https://pdbe.org/8sfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8sfd RCSB], [https://www.ebi.ac.uk/pdbsum/8sfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8sfd ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PHP_SACS2 PHP_SACS2] Has a low paraoxonase activity. Also active, but with a lower activity, against other organo-phosphorus insecticides such as Dursban, Coumaphos, pNP-butanoate or parathion.<ref>PMID:15909078</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Enzymatic promiscuity, the ability of enzymes to catalyze multiple, distinct chemical reactions, has been well documented and is hypothesized to be a major driver of the emergence of new enzymatic functions. Yet, the molecular mechanisms involved in the transition from one activity to another remain debated and elusive. Here, we evaluated the redesign of the active site binding cleft of lactonase SsoPox using structure-based design and combinatorial libraries. We created variants with largely improved catalytic abilities against phosphotriesters, the best ones being >1000-fold better compared to the wild-type enzyme. The observed shifts in activity specificity are large, and some variants completely lost their initial activity. The selected combinations of mutations have considerably reshaped the active site cavity via side chain changes but mostly through large rearrangements of the active site loops and changes to their conformations, as revealed by a suite of crystal structures. This suggests that a specific active site loop configuration is critical to the lactonase activity. Interestingly, analysis of high-resolution structures hints at the potential role of conformational sampling and its directionality in defining the enzyme activity profile. | |||
Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity.,Jacquet P, Billot R, Shimon A, Hoekstra N, Bergonzi C, Jenks A, Chabriere E, Daude D, Elias MH JACS Au. 2024 Apr 25;4(5):1941-1953. doi: 10.1021/jacsau.4c00179. eCollection , 2024 May 27. PMID:38818068<ref>PMID:38818068</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Bergonzi | <div class="pdbe-citations 8sfd" style="background-color:#fffaf0;"></div> | ||
[[Category: Billot | == References == | ||
[[Category: | <references/> | ||
[[Category: Elias | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Jenks | [[Category: Saccharolobus solfataricus P2]] | ||
[[Category: Shimon | [[Category: Bergonzi C]] | ||
[[Category: Billot R]] | |||
[[Category: Daude D]] | |||
[[Category: Elias MH]] | |||
[[Category: Hoekstra N]] | |||
[[Category: Jacquet P]] | |||
[[Category: Jenks A]] | |||
[[Category: Shimon A]] | |||
Latest revision as of 09:27, 4 December 2024
Crystal structure of the engineered SsoPox variant IVB10Crystal structure of the engineered SsoPox variant IVB10
Structural highlights
FunctionPHP_SACS2 Has a low paraoxonase activity. Also active, but with a lower activity, against other organo-phosphorus insecticides such as Dursban, Coumaphos, pNP-butanoate or parathion.[1] Publication Abstract from PubMedEnzymatic promiscuity, the ability of enzymes to catalyze multiple, distinct chemical reactions, has been well documented and is hypothesized to be a major driver of the emergence of new enzymatic functions. Yet, the molecular mechanisms involved in the transition from one activity to another remain debated and elusive. Here, we evaluated the redesign of the active site binding cleft of lactonase SsoPox using structure-based design and combinatorial libraries. We created variants with largely improved catalytic abilities against phosphotriesters, the best ones being >1000-fold better compared to the wild-type enzyme. The observed shifts in activity specificity are large, and some variants completely lost their initial activity. The selected combinations of mutations have considerably reshaped the active site cavity via side chain changes but mostly through large rearrangements of the active site loops and changes to their conformations, as revealed by a suite of crystal structures. This suggests that a specific active site loop configuration is critical to the lactonase activity. Interestingly, analysis of high-resolution structures hints at the potential role of conformational sampling and its directionality in defining the enzyme activity profile. Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity.,Jacquet P, Billot R, Shimon A, Hoekstra N, Bergonzi C, Jenks A, Chabriere E, Daude D, Elias MH JACS Au. 2024 Apr 25;4(5):1941-1953. doi: 10.1021/jacsau.4c00179. eCollection , 2024 May 27. PMID:38818068[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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