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| | ==W229D and F290W mutant of the last common ancestor of Gram-negative bacteria (GNCA4) beta-lactamase class A bound to 5(6)-nitrobenzotriazole (TS-analog)== | | ==W229D and F290W mutant of the last common ancestor of Gram-negative bacteria (GNCA4) beta-lactamase class A bound to 5(6)-nitrobenzotriazole (TS-analog)== |
| - | <StructureSection load='5fqk' size='340' side='right' caption='[[5fqk]], [[Resolution|resolution]] 1.77Å' scene=''> | + | <StructureSection load='5fqk' size='340' side='right'caption='[[5fqk]], [[Resolution|resolution]] 1.77Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5fqk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FQK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5fqk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FQK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6NT:6-NITROBENZOTRIAZOLE'>6NT</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]] 1.767Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5fqi|5fqi]], [[5fqj|5fqj]], [[5fqq|5fqq]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NT:6-NITROBENZOTRIAZOLE'>6NT</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=5fqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqk OCA], [https://pdbe.org/5fqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fqk RCSB], [https://www.ebi.ac.uk/pdbsum/5fqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqk 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=5fqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fqk OCA], [http://pdbe.org/5fqk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fqk RCSB], [http://www.ebi.ac.uk/pdbsum/5fqk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fqk ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Beta-lactamase]] | + | [[Category: Large Structures]] |
| - | [[Category: Synthetic construct sequences]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Gavira, J A]] | + | [[Category: Gavira JA]] |
| - | [[Category: Martinez-Rodriguez, S]] | + | [[Category: Martinez-Rodriguez S]] |
| - | [[Category: Risso, V A]] | + | [[Category: Risso VA]] |
| - | [[Category: Sanchez-Ruiz, J M]] | + | [[Category: Sanchez-Ruiz JM]] |
| - | [[Category: Gnca4]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Precambrian]]
| + | |
| - | [[Category: Resurrected beta-lactamase]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.
De novo active sites for resurrected Precambrian enzymes.,Risso VA, Martinez-Rodriguez S, Candel AM, Kruger DM, Pantoja-Uceda D, Ortega-Munoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM Nat Commun. 2017 Jul 18;8:16113. doi: 10.1038/ncomms16113. PMID:28719578[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Risso VA, Martinez-Rodriguez S, Candel AM, Kruger DM, Pantoja-Uceda D, Ortega-Munoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM. De novo active sites for resurrected Precambrian enzymes. Nat Commun. 2017 Jul 18;8:16113. doi: 10.1038/ncomms16113. PMID:28719578 doi:http://dx.doi.org/10.1038/ncomms16113
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