4MRY

Crystal Structure of Ca(2+)- discharged Y138F obelin mutant from Obelia longissima at 1.30 Angstrom resolution

Summary for 4MRY

• Entry DOI: 10.2210/pdb4mry/pdb
• Related: 1EJ3 1JF2 1QV0 1S36 1SL7 2F8P 4MRX
• Descriptor: Obelin, N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: luminescent protein, calcium binding, ef-hand
• Biological source: Obelia longissima
• Total number of polymer chains: 1
• Total formula weight: 22754.59

Authors

Natashin, P.V.,Ding, W.,Eremeeva, E.V.,Markova, S.V.,Lee, J.,Vysotski, E.S.,Liu, Z.J. (deposition date: 2013-09-17, release date: 2014-03-12, Last modification date: 2023-11-08)

Primary citation

Natashin, P.V.,Ding, W.,Eremeeva, E.V.,Markova, S.V.,Lee, J.,Vysotski, E.S.,Liu, Z.J.
Structures of the Ca2+-regulated photoprotein obelin Y138F mutant before and after bioluminescence support the catalytic function of a water molecule in the reaction.
Acta Crystallogr.,Sect.D, 70:720-732, 2014

PubMed Abstract: Ca(2+)-regulated photoproteins, which are responsible for light emission in a variety of marine coelenterates, are a highly valuable tool for measuring Ca(2+) inside living cells. All of the photoproteins are a single-chain polypeptide to which a 2-hydroperoxycoelenterazine molecule is tightly but noncovalently bound. Bioluminescence results from the oxidative decarboxylation of 2-hydroperoxycoelenterazine, generating protein-bound coelenteramide in an excited state. Here, the crystal structures of the Y138F obelin mutant before and after bioluminescence are reported at 1.72 and 1.30 Å resolution, respectively. The comparison of the spatial structures of the conformational states of Y138F obelin with those of wild-type obelin gives clear evidence that the substitution of Tyr by Phe does not affect the overall structure of both Y138F obelin and its product following Ca(2+) discharge compared with the corresponding conformational states of wild-type obelin. Despite the similarity of the overall structures and internal cavities of Y138F and wild-type obelins, there is a substantial difference: in the cavity of Y138F obelin a water molecule corresponding to W2 in wild-type obelin is not found. However, in Ca(2+)-discharged Y138F obelin this water molecule now appears in the same location. This finding, together with the observed much slower kinetics of Y138F obelin, clearly supports the hypothesis that the function of a water molecule in this location is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion before its decomposition into the excited-state product. Although obelin differs from other hydromedusan Ca(2+)-regulated photoproteins in some of its properties, they are believed to share a common mechanism.

PubMed: 24598741
DOI: 10.1107/S1399004713032434

Experimental method

X-RAY DIFFRACTION (1.299 Å)