6YN2 image
Entry Detail
PDB ID:
6YN2
Title:
Crystal structure of Renilla reniformis luciferase variant RLuc8-W121F/E144Q in complex with a coelenteramide (the postcatalytic enzyme-product complex)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2020-04-10
Release Date:
2021-04-21
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.19
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Coelenterazine h 2-monooxygenase
Chain IDs:A, B
Chain Length:317
Number of Molecules:2
Biological Source:Renilla reniformis
Primary Citation

Abstact

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 AncHLD-RLuc which catalyses both dehalogenase and luciferase reactions. Insertion-deletion (InDel) backbone mutagenesis of AncHLD-RLuc 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.

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