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| | <StructureSection load='6q7r' size='340' side='right'caption='[[6q7r]], [[Resolution|resolution]] 1.50Å' scene=''> | | <StructureSection load='6q7r' size='340' side='right'caption='[[6q7r]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6q7r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q7R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q7R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6q7r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q7R FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AC0:1-PHENYLETHANONE'>AC0</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> | + | </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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AC0:1-PHENYLETHANONE'>AC0</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH0459 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</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=6q7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q7r OCA], [https://pdbe.org/6q7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q7r RCSB], [https://www.ebi.ac.uk/pdbsum/6q7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q7r ProSAT]</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=6q7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q7r OCA], [http://pdbe.org/6q7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q7r RCSB], [http://www.ebi.ac.uk/pdbsum/6q7r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q7r ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/O58216_PYRHO O58216_PYRHO] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrococcus shinkaii]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Levy, C W]] | + | [[Category: Pyrococcus horikoshii]] |
| - | [[Category: Computationally designed enzyme]] | + | [[Category: Levy CW]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
O58216_PYRHO
Publication Abstract from PubMed
The combination of computational design and laboratory evolution is a powerful and potentially versatile strategy for the development of enzymes with new functions(1-4). However, the limited functionality presented by the genetic code restricts the range of catalytic mechanisms that are accessible in designed active sites. Inspired by mechanistic strategies from small-molecule organocatalysis(5), here we report the generation of a hydrolytic enzyme that uses Ndelta-methylhistidine as a non-canonical catalytic nucleophile. Histidine methylation is essential for catalytic function because it prevents the formation of unreactive acyl-enzyme intermediates, which has been a long-standing challenge when using canonical nucleophiles in enzyme design(6-10). Enzyme performance was optimized using directed evolution protocols adapted to an expanded genetic code, affording a biocatalyst capable of accelerating ester hydrolysis with greater than 9,000-fold increased efficiency over free Ndelta-methylhistidine in solution. Crystallographic snapshots along the evolutionary trajectory highlight the catalytic devices that are responsible for this increase in efficiency. Ndelta-methylhistidine can be considered to be a genetically encodable surrogate of the widely employed nucleophilic catalyst dimethylaminopyridine(11), and its use will create opportunities to design and engineer enzymes for a wealth of valuable chemical transformations.
Design and evolution of an enzyme with a non-canonical organocatalytic mechanism.,Burke AJ, Lovelock SL, Frese A, Crawshaw R, Ortmayer M, Dunstan M, Levy C, Green AP Nature. 2019 May 27. pii: 10.1038/s41586-019-1262-8. doi:, 10.1038/s41586-019-1262-8. PMID:31132786[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Burke AJ, Lovelock SL, Frese A, Crawshaw R, Ortmayer M, Dunstan M, Levy C, Green AP. Design and evolution of an enzyme with a non-canonical organocatalytic mechanism. Nature. 2019 May 27. pii: 10.1038/s41586-019-1262-8. doi:, 10.1038/s41586-019-1262-8. PMID:31132786 doi:http://dx.doi.org/10.1038/s41586-019-1262-8
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