5BPJ

All Three Ca(2+)-binding Loops of Light-sensitive Ctenophore Photoprotein Berovin Bind Magnesium Ions: The Spatial Structure of Mg(2+)-loaded Apo-berovin

Summary for 5BPJ

• Entry DOI: 10.2210/pdb5bpj/pdb
• Related: 4MN0
• Descriptor: Apoberovin 1, MAGNESIUM ION (3 entities in total)
• Functional Keywords: luminescent protein, ca(2+)-regulated photoprotein, coelenterazine, berovin, bioluminescent protein, ef-hand, ca(2+)-binding protein, ca(2+)-regulated bioluminescent protein, coelenterazine binding, calcium binding
• Biological source: Beroe abyssicola (Comb jellyfish)
• Total number of polymer chains: 1
• Total formula weight: 24978.71

Authors

Burakova, L.P.,Natashin, P.V.,Malikova, N.P.,Niu, F.,Vysotski, E.S.,Liu, Z.-J. (deposition date: 2015-05-28, release date: 2015-12-30, Last modification date: 2024-01-10)

Primary citation

Burakova, L.P.,Natashin, P.V.,Malikova, N.P.,Niu, F.,Pu, M.,Vysotski, E.S.,Liu, Z.J.
All Ca(2+)-binding loops of light-sensitive ctenophore photoprotein berovin bind magnesium ions: The spatial structure of Mg(2+)-loaded apo-berovin.
J. Photochem. Photobiol. B, Biol., 154:57-66, 2016

PubMed Abstract: Light-sensitive photoprotein berovin accounts for a bright bioluminescence of ctenophore Beroe abyssicola. Berovin is functionally identical to the well-studied Ca(2+)-regulated photoproteins of jellyfish, however in contrast to those it is extremely sensitive to the visible light. Berovin contains three EF-hand Ca(2+)-binding sites and consequently belongs to a large family of the EF-hand Ca(2+)-binding proteins. Here we report the spatial structure of apo-berovin with bound Mg(2+) determined at 1.75Å. The magnesium ion is found in each functional EF-hand loop of a photoprotein and coordinated by oxygen atoms donated by the side-chain groups of aspartate, carbonyl groups of the peptide backbone, or hydroxyl group of serine with characteristic oxygen-Mg(2+) distances. As oxygen supplied by the side-chain of the twelfth residue of all Ca(2+)-binding loops participates in the magnesium ion coordination, it was suggested that Ca(2+)-binding loops of berovin belong to the mixed Ca(2+)/Mg(2+) rather than Ca(2+)-specific type. In addition, we report an effect of physiological concentration of Mg(2+) on bioluminescence of berovin (sensitivity to Ca(2+), rapid-mixed kinetics, light-sensitivity, thermostability, and apo-berovin conversion into active protein). The different impact of physiological concentration of Mg(2+) on berovin bioluminescence as compared to hydromedusan photoproteins was attributed to different affinities of the Ca(2+)-binding sites of these photoproteins to Mg(2+).

PubMed: 26690016
DOI: 10.1016/j.jphotobiol.2015.11.012

Experimental method

X-RAY DIFFRACTION (1.756 Å)