8BO9

NanoLuc-D9R/H57A/K89R mutant complexed with azacoelenterazine bound in intra-barrel catalytic site

Summary for 8BO9

• Entry DOI: 10.2210/pdb8bo9/pdb
• Descriptor: Non structural polyprotein, 3-(4-hydroxyphenyl)-8-[(4-hydroxyphenyl)methyl]-5-(phenylmethyl)-1$l^{4},4,7,8-tetrazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one (3 entities in total)
• Functional Keywords: nanoluc-type luciferase with bound substrate analogue - azacoelenterazine, luminescent protein
• Biological source: synthetic construct
• Total number of polymer chains: 3
• Total formula weight: 62453.25

Authors

Marek, M.,Janin, L.Y. (deposition date: 2022-11-15, release date: 2023-09-27, Last modification date: 2023-12-13)

Primary citation

Nemergut, M.,Pluskal, D.,Horackova, J.,Sustrova, T.,Tulis, J.,Barta, T.,Baatallah, R.,Gagnot, G.,Novakova, V.,Majerova, M.,Sedlackova, K.,Marques, S.M.,Toul, M.,Damborsky, J.,Prokop, Z.,Bednar, D.,Janin, Y.L.,Marek, M.
Illuminating the mechanism and allosteric behavior of NanoLuc luciferase.
Nat Commun, 14:7864-7864, 2023

PubMed Abstract: NanoLuc, a superior β-barrel fold luciferase, was engineered 10 years ago but the nature of its catalysis remains puzzling. Here experimental and computational techniques are combined, revealing that imidazopyrazinone luciferins bind to an intra-barrel catalytic site but also to an allosteric site shaped on the enzyme surface. Structurally, binding to the allosteric site prevents simultaneous binding to the catalytic site, and vice versa, through concerted conformational changes. We demonstrate that restructuration of the allosteric site can boost the luminescent reaction in the remote active site. Mechanistically, an intra-barrel arginine coordinates the imidazopyrazinone component of luciferin, which reacts with O via a radical charge-transfer mechanism, and then it also protonates the resulting excited amide product to form a light-emitting neutral species. Concomitantly, an aspartate, supported by two tyrosines, fine-tunes the blue color emitter to secure a high emission intensity. This information is critical to engineering the next-generation of ultrasensitive bioluminescent reporters.

PubMed: 38030625
DOI: 10.1038/s41467-023-43403-y

Experimental method

X-RAY DIFFRACTION (3.1 Å)