1JF2

Crystal Structure of W92F obelin mutant from Obelia longissima at 1.72 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Violet bioluminescence and fast kinetics from W92F obelin: structure-based proposals for the bioluminescence triggering and the identification of the emitting species.

Vysotski, E.S.Liu, Z.J.Markova, S.V.Blinks, J.R.Deng, L.Frank, L.A.Herko, M.Malikova, N.P.Rose, J.P.Wang, B.C.Lee, J.

(2003) Biochemistry 42: 6013-6024

  • DOI: 10.1021/bi027258h
  • Also Cited By: 2F8P

  • PubMed Abstract: 
  • Obelin from the hydroid Obelia longissima and aequorin are members of a subfamily of Ca(2+)-regulated photoproteins that is a part of the larger EF-hand calcium binding protein family. On the addition of Ca(2+), obelin generates a blue bioluminescenc ...

    Obelin from the hydroid Obelia longissima and aequorin are members of a subfamily of Ca(2+)-regulated photoproteins that is a part of the larger EF-hand calcium binding protein family. On the addition of Ca(2+), obelin generates a blue bioluminescence emission (lambda(max) = 485 nm) as the result of the oxidative decarboxylation of the bound substrate, coelenterazine. The W92F obelin mutant is noteworthy because of the unusually high speed with which it responds to sudden changes of [Ca(2+)] and because it emits violet light rather than blue due to a prominent band with lambda(max) = 405 nm. Increase of pH in the range from 5.5 to 8.5 and using D(2)O both diminish the contribution of the 405 nm band, indicating that excited state proton transfer is involved. Fluorescence model studies have suggested the origin of the 485 nm emission as the excited state of an anion of coelenteramide, the bioluminescence reaction product, and 405 nm from the excited neutral state. Assuming that the dimensions of the substrate binding cavity do not change during the excited state formation, a His22 residue within hydrogen bonding distance to the 6-(p-hydroxy)-phenyl group of the excited coelenteramide is a likely candidate for accepting the phenol proton to produce an ion-pair excited state, in support of recent suggestions for the bioluminescence emitting state. The proton transfer could be impeded by removal of the Trp92 H-bond, resulting in strong enhancement of a 405 nm band giving the violet color of bioluminescence. Comparative analysis of 3D structures of the wild-type (WT) and W92F obelins reveals that there are structural displacements of certain key Ca(2+)-ligating residues in the loops of the two C-terminal EF hands as well as clear differences in hydrogen bond networks in W92F. For instance, the hydrogen bond between the side-chain oxygen atom of Asp169 and the main-chain nitrogen of Arg112 binds together the incoming alpha-helix of loop III and the exiting alpha-helix of loop IV in WT, providing probably concerted changes in these EF hands on calcium binding. But this linkage is not found in W92F obelin. These differences apparently do not change the overall affinity to calcium of W92F obelin but may account for the kinetic differences between the WT and mutant obelins. From analysis of the hydrogen bond network in the coelenterazine binding cavity, it is proposed that the trigger for bioluminescence reaction in these Ca(2+)-regulated photoproteins may be a shift of the hydrogen bond donor-acceptor separations around the coelenterazine-2-hydroperoxy substrate, initiated by small spatial adjustment of the exiting alpha-helix of loop IV.


    Related Citations: 
    • Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure.
      Liu, Z.J.,Vysotski, E.S.,Chen, C.J.,Rose, J.P.,Lee, J.,Wang, B.C.
      (2000) Protein Sci. 9: 2085
    • Obelin crystal structure: implications for the bioluminescence mechanism
      Vysotski, E.,Liu, Z.-J.,Deng, L.,Rose, J.,Wang, B.-C.,Lee, J.
      (2001) Bioluminescence and Chemiluminescence 2000 --: --
    • Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima.
      Vysotski, E.S.,Liu, Z.J.,Rose, J.,Wang, B.C.,Lee, J.
      (1999) Acta Crystallogr.,Sect.D 55: 1965


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
obelin
A
195Obelia longissimaMutations: F92W
Find proteins for Q27709 (Obelia longissima)
Go to UniProtKB:  Q27709
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CZH
Query on CZH

Download SDF File 
Download CCD File 
A
C2-HYDROPEROXY-COELENTERAZINE
8-BENZYL-2-HYDROPEROXY-2-(4-HYDROXY-BENZYL)-6-(4-HYDROXY-PHENYL)-2H-IMIDAZO[1,2-A]PYRAZIN-3-ONE
C26 H21 N3 O5
HOSWCJDTHOAORT-SANMLTNESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.232 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.449α = 90.00
b = 53.449β = 90.00
c = 144.485γ = 90.00
Software Package:
Software NamePurpose
Crystaldata collection
CNSrefinement
SCALEPACKdata scaling
CrystalCleardata reduction
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-02-19
    Type: Database references