6WI4 | pdb_00006wi4

Caspases from Scleractinian Coral


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Caspases from scleractinian coral show unique regulatory features.

Shrestha, S.Tung, J.Grinshpon, R.D.Swartz, P.Hamilton, P.T.Dimos, B.Mydlarz, L.Clark, A.C.

(2020) J Biological Chem 295: 14578-14591

  • DOI: https://doi.org/10.1074/jbc.RA120.014345
  • Primary Citation Related Structures: 
    6WI4

  • PubMed Abstract: 

    Coral reefs are experiencing precipitous declines around the globe with coral diseases and temperature-induced bleaching being primary drivers of these declines. Regulation of apoptotic cell death is an important component in the coral stress response. Although cnidaria are known to contain complex apoptotic signaling pathways, similar to those in vertebrates, the mechanisms leading to cell death are largely unexplored. We identified and characterized two caspases each from Orbicella faveolata , a disease-sensitive reef-building coral, and Porites astreoides , a disease-resistant reef-building coral. The caspases are predicted homologs of the human executioner caspases-3 and -7, but OfCasp3a ( Orbicella faveolata caspase-3a) and PaCasp7a ( Porites astreoides caspase-7a), which we show to be D XX Dases, contain an N-terminal caspase activation/recruitment domain (CARD) similar to human initiator/inflammatory caspases. OfCasp3b ( Orbicella faveolata caspase-3b) and PaCasp3 ( Porites astreoides caspase-3), which we show to be V XX Dases, have short pro-domains, like human executioner caspases. Our biochemical analyses suggest a mechanism in coral which differs from that of humans, where the CARD-containing D XX Dase is activated on death platforms but the protease does not directly activate the V XX Dase. The first X-ray crystal structure of a coral caspase, of PaCasp7a determined at 1.57 Å resolution, reveals a conserved fold and an N-terminal peptide bound near the active site that may serve as a regulatory exosite. The binding pocket has been observed in initiator caspases of other species. These results suggest mechanisms for the evolution of substrate selection while maintaining common activation mechanisms of CARD-mediated dimerization.


  • Organizational Affiliation
    • Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.

Macromolecule Content 

  • Total Structure Weight: 55.46 kDa 
  • Atom Count: 4,404 
  • Modeled Residue Count: 483 
  • Deposited Residue Count: 483 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-3
A, B
233Porites astreoidesMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-37Porites astreoidesMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ACE-DEVD inhibitor
D, E
5Porites astreoidesMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.416α = 90
b = 86.848β = 90
c = 93.666γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM127654

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary