5VP3

Light-sensitive photoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations.

Molakarimi, M.Gorman, M.A.Mohseni, A.Pashandi, Z.Taghdir, M.Naderi-Manesh, H.Sajedi, R.H.Parker, M.W.

(2019) J Biol Chem 294: 20-27

  • DOI: https://doi.org/10.1074/jbc.RA118.006053
  • Primary Citation of Related Structures:  
    5VP3

  • PubMed Abstract: 

    Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca 2+ -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 2+ -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.


  • Organizational Affiliation

    Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mnemiopsin 1206Mnemiopsis leidyiMutation(s): 0 
Gene Names: PP1
UniProt
Find proteins for E0WVU4 (Mnemiopsis leidyi)
Explore E0WVU4 
Go to UniProtKB:  E0WVU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0WVU4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.614α = 90
b = 72.614β = 90
c = 81.429γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 2.0: 2019-01-16
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description