1UHI

Crystal structure of i-aequorin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structures of semi-synthetic aequorins

Toma, S.Chong, K.T.Nakagawa, A.Teranishi, K.Inouye, S.Shimomura, O.

(2005) Protein Sci. 14: 409-416

  • DOI: 10.1110/ps.041067805
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The photoprotein aequorin emits light by an intramolecular reaction in the presence of a trace amount of Ca(2+). Semi-synthetic aequorins, produced by replacing the coelenterazine moiety in aequorin with the analogues of coelenterazine, show widely d ...

    The photoprotein aequorin emits light by an intramolecular reaction in the presence of a trace amount of Ca(2+). Semi-synthetic aequorins, produced by replacing the coelenterazine moiety in aequorin with the analogues of coelenterazine, show widely different sensitivities to Ca(2+). To understand the structural basis of the Ca(2+)-sensitivity, we determined the crystal structures of four semi-synthetic aequorins (cp-, i-, br- and n-aequorins) at resolutions of 1.6-1.8 A. In general, the protein structures of these semi-synthetic aequorins are almost identical to native aequorin. Of the four EF-hand domains in the molecule, EF-hand II does not bind Ca(2+), and the loop of EF-hand IV is clearly deformed. It is most likely that the binding of Ca(2+) with EF-hands I and III triggers luminescence. Although little difference was found in the overall structures of aequorins investigated, some significant differences were found in the interactions between the substituents of coelenterazine moiety and the amino acid residues in the binding pocket. The coelenterazine moieties in i-, br-, and n-aequorins have bulky 2-substitutions, which can interfere with the conformational changes of protein structure that follow the binding of Ca(2+) to aequorin. In cp-aequorin, the cyclopentylmethyl group that substitutes for the original 8-benzyl group does not interact hydrophobically with the protein part, giving the coelenterazine moiety more conformational freedom to promote the light-emitting reaction. The differences of various semi-synthetic aequorins in Ca(2+)-sensitivity and reaction rate are explained by the capability of the involved groups and structures to undergo conformational changes in response to the Ca(2+)-binding.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aequorin 2
A, B
191Aequorea victoriaMutation(s): 0 
Find proteins for P02592 (Aequorea victoria)
Go to UniProtKB:  P02592
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CZI
Query on CZI

Download SDF File 
Download CCD File 
A, B
(2R)-8-BENZYL-2-HYDROPEROXY-6-(4-HYDROXYPHENYL)-2-(4-IODOBENZYL)-7,8-DIHYDROIMIDAZO[1,2-A]PYRAZIN-3(2H)-ONE
I-COELENETERAZINE
C26 H22 I N3 O4
VKJBKKSOPAEBAT-GJZUVCINSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.188 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 34.263α = 102.05
b = 54.432β = 99.70
c = 57.523γ = 103.80
Software Package:
Software NamePurpose
d*TREKdata reduction
REFMACrefinement
MOLREPphasing
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance