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| | ==Crystal structure of Diels-Alderase CE20 in complex with a product analog== | | ==Crystal structure of Diels-Alderase CE20 in complex with a product analog== |
| - | <StructureSection load='4o5t' size='340' side='right' caption='[[4o5t]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='4o5t' size='340' side='right'caption='[[4o5t]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4o5t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_european_squid Common european squid]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5T FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4o5t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Loligo_vulgaris Loligo vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O5T FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XDA:4-{[2-(PHOSPHONOOXY)ETHYL]CARBAMOYL}BENZYL+[(1R,6S)-6-(DIMETHYLCARBAMOYL)CYCLOHEX-2-EN-1-YL]CARBAMATE'>XDA</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]] 2.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3u0s|3u0s]], [[3i1c|3i1c]], [[1e1a|1e1a]], [[4o5s|4o5s]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XDA:4-{[2-(PHOSPHONOOXY)ETHYL]CARBAMOYL}BENZYL+[(1R,6S)-6-(DIMETHYLCARBAMOYL)CYCLOHEX-2-EN-1-YL]CARBAMATE'>XDA</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diisopropyl-fluorophosphatase Diisopropyl-fluorophosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.2 3.1.8.2] </span></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=4o5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5t OCA], [https://pdbe.org/4o5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o5t RCSB], [https://www.ebi.ac.uk/pdbsum/4o5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5t 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=4o5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5t OCA], [http://pdbe.org/4o5t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o5t RCSB], [http://www.ebi.ac.uk/pdbsum/4o5t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5t ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DFPA_LOLVU DFPA_LOLVU]] Biological function and substrate unknown. However, it is capable of acting on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including nerve gases).<ref>PMID:15966726</ref> | + | [https://www.uniprot.org/uniprot/DFPA_LOLVU DFPA_LOLVU] Biological function and substrate unknown. However, it is capable of acting on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including nerve gases).<ref>PMID:15966726</ref> |
| | <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: Common european squid]] | + | [[Category: Large Structures]] |
| - | [[Category: Diisopropyl-fluorophosphatase]] | + | [[Category: Loligo vulgaris]] |
| - | [[Category: Beck, T]] | + | [[Category: Beck T]] |
| - | [[Category: Hilvert, D]] | + | [[Category: Hilvert D]] |
| - | [[Category: Mayer, C]] | + | [[Category: Mayer C]] |
| - | [[Category: Preiswerk, N]] | + | [[Category: Preiswerk N]] |
| - | [[Category: Artificial catalyst]]
| + | |
| - | [[Category: Beta-propeller]]
| + | |
| - | [[Category: Catalyst for cycloaddition]]
| + | |
| - | [[Category: Computer-aided design]]
| + | |
| - | [[Category: De novo protein]]
| + | |
| - | [[Category: Diels-alder reaction]]
| + | |
| - | [[Category: Diels-alderase]]
| + | |
| - | [[Category: Directed evolution]]
| + | |
| - | [[Category: Enzyme design]]
| + | |
| - | [[Category: Enzyme-product analog complexes']]
| + | |
| - | [[Category: Helix-loop-helix]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Protein engineering]]
| + | |
| - | [[Category: Substrate specificity]]
| + | |
| Structural highlights
Function
DFPA_LOLVU Biological function and substrate unknown. However, it is capable of acting on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including nerve gases).[1]
Publication Abstract from PubMed
By combining targeted mutagenesis, computational refinement, and directed evolution, a modestly active, computationally designed Diels-Alderase was converted into the most proficient biocatalyst for [4+2] cycloadditions known. The high stereoselectivity and minimal product inhibition of the evolved enzyme enabled preparative scale synthesis of a single product diastereomer. X-ray crystallography of the enzyme-product complex shows that the molecular changes introduced over the course of optimization, including addition of a lid structure, gradually reshaped the pocket for more effective substrate preorganization and transition state stabilization. The good overall agreement between the experimental structure and the original design model with respect to the orientations of both the bound product and the catalytic side chains contrasts with other computationally designed enzymes. Because design accuracy appears to correlate with scaffold rigidity, improved control over backbone conformation will likely be the key to future efforts to design more efficient enzymes for diverse chemical reactions.
Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase.,Preiswerk N, Beck T, Schulz JD, Milovnik P, Mayer C, Siegel JB, Baker D, Hilvert D Proc Natl Acad Sci U S A. 2014 May 20. pii: 201401073. PMID:24847076[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Katsemi V, Lucke C, Koepke J, Lohr F, Maurer S, Fritzsch G, Ruterjans H. Mutational and structural studies of the diisopropylfluorophosphatase from Loligo vulgaris shed new light on the catalytic mechanism of the enzyme. Biochemistry. 2005 Jun 28;44(25):9022-33. PMID:15966726 doi:10.1021/bi0500675
- ↑ Preiswerk N, Beck T, Schulz JD, Milovnik P, Mayer C, Siegel JB, Baker D, Hilvert D. Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase. Proc Natl Acad Sci U S A. 2014 May 20. pii: 201401073. PMID:24847076 doi:http://dx.doi.org/10.1073/pnas.1401073111
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