2F8P

Crystal structure of obelin following Ca2+ triggered bioluminescence suggests neutral coelenteramide as the primary excited state

Summary for 2F8P

• Entry DOI: 10.2210/pdb2f8p/pdb
• Related: 1EL4 1JF0 1JF2 1QV0 1S36 1SL7
• Descriptor: Obelin, CALCIUM ION, N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE, ... (4 entities in total)
• Functional Keywords: helix-turn-helix, structural genomics, psi, protein structure initiative, southeast collaboratory for structural genomics, secsg, luminescent protein
• Biological source: Obelia longissima
• Total number of polymer chains: 1
• Total formula weight: 22770.59

Authors

Liu, Z.J.,Stepanyuk, G.A.,Vysotski, E.S.,Lee, J.,Wang, B.C.,Southeast Collaboratory for Structural Genomics (SECSG) (deposition date: 2005-12-03, release date: 2006-02-14, Last modification date: 2023-08-30)

Primary citation

Liu, Z.J.,Stepanyuk, G.A.,Vysotski, E.S.,Lee, J.,Markova, S.V.,Malikova, N.P.,Wang, B.C.
Crystal structure of obelin after Ca2+-triggered bioluminescence suggests neutral coelenteramide as the primary excited state.
Proc.Natl.Acad.Sci.Usa, 103:2570-2575, 2006

PubMed Abstract: The crystal structure at 1.93-A resolution is determined for the Ca2+-discharged obelin containing three bound calcium ions as well as the product of the bioluminescence reaction, coelenteramide. This finding extends the series of available spatial structures of the ligand-dependent conformations of the protein to four, the obelin itself, and those after the bioluminescence reaction with or without bound Ca2+ and/or coelenteramide. Among these structures, global conformational changes are small, typical of the class of "calcium signal modulators" within the EF-hand protein superfamily. Nevertheless, in the active site there are significant repositions of two residues. The His-175 imidazole ring flips becoming almost perpendicular to the original orientation corroborating the crucial importance of this residue for triggering bioluminescence. Tyr-138 hydrogen bonded to the coelenterazine N1-atom in unreacted obelin is moved away from the binding cavity after reaction. However, this Tyr is displaced by a water molecule from within the cavity, which now forms a hydrogen bond to the same atom, the amide N of coelenteramide. From this observation, a reaction scheme is proposed that would result in the neutral coelenteramide as the primary excited state product in photoprotein bioluminescence. From such a higher energy state it is now energetically feasible to account for the shorter wavelength bioluminescence spectra obtained from some photoprotein mutants or to populate the lower energy state of the phenolate anion to yield the blue bioluminescence ordinarily observed from native photoproteins.

PubMed: 16467137
DOI: 10.1073/pnas.0511142103

Experimental method

X-RAY DIFFRACTION (1.93 Å)