PDBsum entry 5bpj

Luminescent protein

PDB id: 5bpj

Contents

Protein chain

180 a.a.

Metals

_MG ×3

Waters ×97

PDB id:

5bpj

Name:

Luminescent protein

Title:

All three ca(2+)-binding loops of light-sensitive ctenophore photoprotein berovin bind magnesium ions: the spatial structure of mg(2+)-loaded apo-berovin

Structure:

Apoberovin 1. Chain: a. Synonym: apoberovin 2,apoberovin 3,apoberovin 4. Engineered: yes

Source:

Beroe abyssicola. Comb jellyfish. Organism_taxid: 320166. Gene: ba2, ba1, ba3, ba4. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.76Å R-factor: 0.225 R-free: 0.243

Authors:

L.P.Burakova,P.V.Natashin,N.P.Malikova,F.Niu,E.S.Vysotski,Z.-J.Liu

Key ref:

L.P.Burakova et al. (2016). 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, 154, 57-66. PubMed id: 26690016 DOI: 10.1016/j.jphotobiol.2015.11.012

Date:

28-May-15 Release date: 30-Dec-15

Protein chain

H8ZZK1  (H8ZZK1_BERAB) -  Apoberovin 1 from Beroe abyssicola

Seq: 208 a.a.

Struc: 180 a.a.

DOI no: 10.1016/j.jphotobiol.2015.11.012

J Photochem Photobiol B 154:57-66 (2016)

PubMed id: 26690016

All Ca(2+)-binding loops of light-sensitive ctenophore photoprotein berovin bind magnesium ions: The spatial structure of Mg(2+)-loaded apo-berovin.

L.P.Burakova, P.V.Natashin, N.P.Malikova, F.Niu, M.Pu, E.S.Vysotski, Z.J.Liu.

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+).