1SL7

Crystal structure of calcium-loaded apo-obelin from Obelia longissima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

All three Ca2+-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin.

Deng, L.Vysotski, E.S.Markova, S.V.Liu, Z.J.Lee, J.Rose, J.Wang, B.C.

(2005) Protein Sci. 14: 663-675

  • DOI: 10.1110/ps.041142905
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of calcium-loaded apo-aequorin and apo-obelin have been determined at resolutions 1.7A and 2.2 A, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and ...

    The crystal structures of calcium-loaded apo-aequorin and apo-obelin have been determined at resolutions 1.7A and 2.2 A, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-protein retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hyroperoxycoelenterazine, and also the same as the Ca2+-discharged obelin bound with product, coleneteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.


    Related Citations: 
    • Structure of the Ca2+-regulated photoprotein obelin at 1.7 resolution determined directly from its sulfur substructure
      Liu, Z.-J.,Vysotski, E.S.,Chen, C.-J.,Rose, J.,Lee, J.,Wang, B.-C.
      (2000) Protein Sci. 9: 2085
    • 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.,Deng, L.,Frank, L.A.,Herko, M.,Malikova, N.P.,Rose, J.P.,Wang, B.-C.,Lee, J.
      (2003) Biochemistry 42: 6013
    • Atomic resolution structure of obelin: Soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine
      Liu, Z.-J.,Vysotski, E.S.,Deng, L.,Lee, J.,Rose, J.,Wang, B.-C.
      (2003) Biochem.Biophys.Res.Commun. 311: 433
    • Structural basis for the emission of violet bioluminescence from a W92F obelin mutant
      Deng, L.,Vysotski, E.S.,Liu, Z.-J.,Markova, S.V.,Malikova, N.P.,Lee, J.,Rose, J.,Wang, B.-C.
      (2001) FEBS Lett. 506: 281
    • 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
    • Preparation and X-ray Crystallographic Analysis of the Ca2+-discharged Photoprotein Obelin
      Deng, L.,Markova, S.V.,Vysotski, E.S.,Liu, Z.-J.,Lee, J.,Rose, J.,Wang, B.-C.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Obelin
A
195Obelia longissimaMutation(s): 0 
Find proteins for Q27709 (Obelia longissima)
Go to UniProtKB:  Q27709
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.641α = 90.00
b = 58.641β = 90.00
c = 110.378γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance