8A9S

Crystal structure of Ca2+-discharged obelin in complex with coelenteramine-v

Summary for 8A9S

• Entry DOI: 10.2210/pdb8a9s/pdb
• Descriptor: Obelin, 3-azanyl-2-(phenylmethyl)benzo[f]quinoxalin-8-ol, SODIUM ION, ... (5 entities in total)
• Functional Keywords: bioluminescence, photoprotein, obelin, coelenterazine analogue, coelenterazine-v, luminescent protein
• Biological source: Obelia longissima
• Total number of polymer chains: 2
• Total formula weight: 45627.27

Authors

Kovaleva, M.I.,Natashin, P.V.,Schevtsov, M.B.,Eremeeva, E.V.,Bukhdruker, S.S.,Dmitrieva, D.A.,Mishin, A.V.,Vysotski, E.S.,Borshchevskiy, V.I. (deposition date: 2022-06-29, release date: 2022-10-19, Last modification date: 2024-01-31)

Primary citation

Natashin, P.V.,Eremeeva, E.V.,Shevtsov, M.B.,Kovaleva, M.I.,Bukhdruker, S.S.,Dmitrieva, D.A.,Gulnov, D.V.,Nemtseva, E.V.,Gordeliy, V.I.,Mishin, A.V.,Borshchevskiy, V.I.,Vysotski, E.S.
Crystal structure of semi-synthetic obelin-v after calcium induced bioluminescence implies coelenteramine as the main reaction product.
Sci Rep, 12:19613-19613, 2022

PubMed Abstract: Coelenterazine-v (CTZ-v), a synthetic vinylene-bridged π-extended derivative, is able to significantly alter bioluminescence spectra of different CTZ-dependent luciferases and photoproteins by shifting them towards longer wavelengths. However, Ca-regulated photoproteins activated with CTZ-v display very low bioluminescence activities that hampers its usage as a substrate of photoprotein bioluminescence. Here, we report the crystal structure of semi-synthetic Ca-discharged obelin-v bound with the reaction product determined at 2.1 Å resolution. Comparison of the crystal structure of Ca-discharged obelin-v with those of other obelins before and after bioluminescence reaction reveals no considerable changes in the overall structure. However, the drastic changes in CTZ-binding cavity are observed owing to the completely different reaction product, coelenteramine-v (CTM-v). Since CTM-v is certainly the main product of obelin-v bioluminescence and is considered to be a product of the "dark" pathway of dioxetanone intermediate decomposition, it explains the low bioluminescence activity of obelin and apparently of other photoproteins with CTZ-v.

PubMed: 36379962
DOI: 10.1038/s41598-022-24117-5

Experimental method

X-RAY DIFFRACTION (2.1 Å)