7O3U

The crystal structure of obelin from Obelia longissima bound with v-coelenterazine

Summary for 7O3U

• Entry DOI: 10.2210/pdb7o3u/pdb
• Descriptor: Obelin, v-coelenterazine, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: bioluminescence, coelenterazine, v-coelenterazine, calcium binding, luminescent protein
• Biological source: Obelia longissima (Black sea hydrozoan, Laomedea longissima)
• Total number of polymer chains: 1
• Total formula weight: 22758.47

Authors

Larionova, M.D.,Wu, L.J.,Vysotski, E.S.,Liu, Z.-J. (deposition date: 2021-04-03, release date: 2022-02-09, Last modification date: 2024-01-31)

Primary citation

Larionova, M.D.,Wu, L.,Eremeeva, E.V.,Natashin, P.V.,Gulnov, D.V.,Nemtseva, E.V.,Liu, D.,Liu, Z.J.,Vysotski, E.S.
Crystal structure of semisynthetic obelin-v.
Protein Sci., 31:454-469, 2022

PubMed Abstract: Coelenterazine-v (CTZ-v), a synthetic derivative with an additional benzyl ring, yields a bright bioluminescence of Renilla luciferase and its "yellow" mutant with a significant shift in the emission spectrum toward longer wavelengths, which makes it the substrate of choice for deep tissue imaging. Although Ca -regulated photoproteins activated with CTZ-v also display red-shifted light emission, in contrast to Renilla luciferase their bioluminescence activities are very low, which makes photoproteins activated by CTZ-v unusable for calcium imaging. Here, we report the crystal structure of Ca -regulated photoprotein obelin with 2-hydroperoxycoelenterazine-v (obelin-v) at 1.80 Å resolution. The structures of obelin-v and obelin bound with native CTZ revealed almost no difference; only the minor rearrangement in hydrogen-bond pattern and slightly increased distances between key active site residues and some atoms of 2-hydroperoxycoelenterazine-v were found. The fluorescence quantum yield (Φ ) of obelin bound with coelenteramide-v (0.24) turned out to be even higher than that of obelin with native coelenteramide (0.19). Since both obelins are in effect the enzyme-substrate complexes containing the 2-hydroperoxy adduct of CTZ-v or CTZ, we reasonably assume the chemical reaction mechanisms and the yields of the reaction products (Φ ) to be similar for both obelins. Based on these findings we suggest that low bioluminescence activity of obelin-v is caused by the low efficiency of generating an electronic excited state (Φ ). In turn, the low Φ value as compared to that of native CTZ might be the result of small changes in the substrate microenvironment in the obelin-v active site.

PubMed: 34802167
DOI: 10.1002/pro.4244

Experimental method

X-RAY DIFFRACTION (1.8 Å)