6YN2
Crystal structure of Renilla reniformis luciferase variant RLuc8-W121F/E144Q in complex with a coelenteramide (the postcatalytic enzyme-product complex)
Summary for 6YN2
| Entry DOI | 10.2210/pdb6yn2/pdb |
| Descriptor | Coelenterazine h 2-monooxygenase, N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE, ACETATE ION, ... (6 entities in total) |
| Functional Keywords | bioluminscence, coelenteramide-bound enzyme, luminescent protein |
| Biological source | Renilla reniformis (Sea pansy) |
| Total number of polymer chains | 2 |
| Total formula weight | 74827.45 |
| Authors | Damborsky, J.,Marek, M. (deposition date: 2020-04-10, release date: 2021-04-21, Last modification date: 2024-01-24) |
| Primary citation | Schenkmayerova, A.,Pinto, G.P.,Toul, M.,Marek, M.,Hernychova, L.,Planas-Iglesias, J.,Daniel Liskova, V.,Pluskal, D.,Vasina, M.,Emond, S.,Dorr, M.,Chaloupkova, R.,Bednar, D.,Prokop, Z.,Hollfelder, F.,Bornscheuer, U.T.,Damborsky, J. Engineering the protein dynamics of an ancestral luciferase. Nat Commun, 12:3616-3616, 2021 Cited by PubMed Abstract: Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein Anc which catalyses both dehalogenase and luciferase reactions. Insertion-deletion (InDel) backbone mutagenesis of Anc challenged the scaffold dynamics. Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). An anisotropic network model highlights the importance of the conformational flexibility of a loop-helix fragment of Renilla luciferases for ligand binding. Transplantation of this dynamic fragment leads to lower product inhibition and highly stable glow-type bioluminescence. The success of our approach suggests that a strategy comprising (i) constructing a stable and evolvable template, (ii) mapping functional regions by backbone mutagenesis, and (iii) transplantation of dynamic features, can lead to functionally innovative proteins. PubMed: 34127663DOI: 10.1038/s41467-021-23450-z PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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