5VP3

Light-sensitive photoprotein

5VP3 の概要

• エントリーDOI: 10.2210/pdb5vp3/pdb
• 分子名称: Mnemiopsin 1, CADMIUM ION, NICKEL (II) ION, ... (5 entities in total)
• 機能のキーワード: bioluminescence, ctenophore, ca(2+)-regulated photoprotein, ef-hand, mnemiopsis leidyi, mnemiopsin 1, luminescent protein
• 由来する生物種: Mnemiopsis leidyi (Sea walnut)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 25158.00

構造登録者

Gorman, M.A.,Parker, M.W. (登録日: 2017-05-04, 公開日: 2018-05-09, 最終更新日: 2023-10-04)

主引用文献

Molakarimi, M.,Gorman, M.A.,Mohseni, A.,Pashandi, Z.,Taghdir, M.,Naderi-Manesh, H.,Sajedi, R.H.,Parker, M.W.
Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations.
J. Biol. Chem., 294:20-27, 2019

PubMed Abstract: Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca-dependent photoproteins. The mechanism of light emission operates via the same reaction in both animal families. Despite numerous studies on the ctenophore photoprotein family, the detailed catalytic mechanism and arrangement of amino acid residues surrounding the chromophore in this family are a mystery. Here, we report the crystal structure of Cd-loaded apo-mnemiopsin1, a member of the ctenophore family, at 2.15 Å resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction mechanism. The simulations suggested that an Asp-156-Arg-39-Tyr-202 triad creates a hydrogen-bonded network to facilitate the transfer of a proton from the 2-hydroperoxy group of the chromophore coelenterazine to bulk solvent. We identified a water molecule in the coelenteramide-binding cavity that forms a hydrogen bond with the amide nitrogen atom of coelenteramide, which, in turn, is hydrogen-bonded via another water molecule to Tyr-131. This observation supports the hypothesis that the function of the coelenteramide-bound water molecule is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion, thereby triggering the bioluminescence reaction in the ctenophore photoprotein family.

PubMed: 30420427
DOI: 10.1074/jbc.RA118.006053

実験手法

X-RAY DIFFRACTION (2.151 Å)