PDBsum entry 1uhi

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Luminescent protein PDB id
Protein chains
191 a.a. *
CZI ×2
Waters ×488
* Residue conservation analysis
PDB id:
Name: Luminescent protein
Title: Crystal structure of i-aequorin
Structure: Aequorin 2. Chain: a, b. Synonym: aequorin. Engineered: yes
Source: Aequorea victoria. Organism_taxid: 6100. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.80Å     R-factor:   0.191     R-free:   0.250
Authors: S.Toma,K.T.Chong,A.Nakagawa,K.Teranishi,S.Inouye,O.Shimomura
Key ref:
S.Toma et al. (2005). The crystal structures of semi-synthetic aequorins. Protein Sci, 14, 409-416. PubMed id: 15632284 DOI: 10.1110/ps.041067805
03-Jul-03     Release date:   08-Feb-05    
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Protein chains
Pfam   ArchSchema ?
P02592  (AEQ2_AEQVI) -  Aequorin-2
196 a.a.
191 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     bioluminescence   1 term 
  Biochemical function     metal ion binding     2 terms  


DOI no: 10.1110/ps.041067805 Protein Sci 14:409-416 (2005)
PubMed id: 15632284  
The crystal structures of semi-synthetic aequorins.
S.Toma, K.T.Chong, A.Nakagawa, K.Teranishi, S.Inouye, O.Shimomura.
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.
  Selected figure(s)  
Figure 2.
Figure 2. Structural comparison of native aequorin, semi-synthetic aequorins, and calmodulin. (A) Superimposed structures of molecule A of native aequorin and semi-synthetic aequorins. Native, cp-, br-, i-, and n-aequorin are shown in yellow, pink, blue, sky blue, and green, respectively. Apoaequorins are shown as C trace models. Coelenterazine moieties are drawn as ball-and-stick models with same colors as above. The coelenterazine moiety and the loop region of EF-hands I, III, and IV are surrounded by red, light blue, green, and orange circles, respectively. W1 in native aequorin is drawn as a sphere model in cyan. The OH group of the 2-substituent of native coelenterazine is stabilized by a hydrogen-bonding network mediated by W1. W1 is absent in br-, i-, and n-aequorin. The cyclopentyl group at the C8 position of cp-coelenterazine can make neither a stacking interaction with Lys39 nor a - interaction with Trp108. This figure was prepared with MolScript (Kraulis 1991) and Raster3D (Merrit and Bacon 1997). (B) Superimposed structures of EF-hands I, III, and IV of aequorin. (1) The superimposed structures of EF-hands I (shown in sky blue circle in Fig. 2A: 20-37), III (shown in green circle in Fig. 2A: 113-130), and IV (shown in orange circle in Fig. 2A: 149-166). EF-hand IV in molecule A is colored cyan and EF-hand IV in molecule B is colored blue. EF-hands I and III are colored green and yellow-green, respectively. The blue dashed line, EF-IV(B2), is the loop structure of EF-hand-IV(B) superimposed onto the same region of EF-IV(A). (2) The superimposed structures of the EF-hand I loop (residues 20-37) of aequorin (green) and Ca^2+-bound (deep pink) and Ca^2+-unbound (cream) calmodulin. The Ca^2+ is drawn as a sphere. All figures were prepared with MolScript (Kraulis 1991). (C) Structure comparison between aequorin and calmodulin. The superimposed structures of aequorin (yellow-green) and Ca^2+-unbound calmodulin (cream). The traced region of aequorin is from Thr103 to Pro189. The traced region of calmodulin is from Ser81 to Lys148. The coelenterazine moiety (CZH) is drawn as a ball-and-stick model. Dashed lines appeared in the inside of the red circle are main-chain interactions, green dotted lines are interactions in aequorin, and cream ones are interactions in calmodulin.
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2005, 14, 409-416) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19060386 S.Inouye, and J.Sato (2008).
Comparison of luminescent immunoassays using biotinylated proteins of aequorin, alkaline phosphatase and horseradish peroxidase as reporters.
  Biosci Biotechnol Biochem, 72, 3310-3313.  
16769886 L.Tricoire, K.Tsuzuki, O.Courjean, N.Gibelin, G.Bourout, J.Rossier, and B.Lambolez (2006).
Calcium dependence of aequorin bioluminescence dissected by random mutagenesis.
  Proc Natl Acad Sci U S A, 103, 9500-9505.  
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