6BDV

Crystal structure of Caspase 3 S150A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.938 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Modifications to a common phosphorylation network provide individualized control in caspases.

Thomas, M.E.Grinshpon, R.Swartz, P.Clark, A.C.

(2018) J. Biol. Chem. --: --

  • DOI: 10.1074/jbc.RA117.000728
  • Primary Citation of Related Structures:  6BFJ, 6BFK, 6BFL, 6BFO, 6BG0, 6BG1, 6BG4, 6BGK, 6BGQ, 6BGR, 6BGS, 6BH9, 6BHA

  • PubMed Abstract: 
  • Caspase-3 activation and function has been well defined during programmed cell death, but caspase activity, at low levels, is also required for developmental processes such as lymphoid proliferation and erythroid differentiation. Post-translational m ...

    Caspase-3 activation and function has been well defined during programmed cell death, but caspase activity, at low levels, is also required for developmental processes such as lymphoid proliferation and erythroid differentiation. Post-translational modification of caspase-3 is one method used by cells to fine-tune activity below the threshold required for apoptosis, but the allosteric mechanism that reduces activity is unknown. Phosphorylation of caspase-3 at a conserved allosteric site by p38-MAPK promotes survival in human neutrophils, and the modification of the loop is thought to be a key regulator in many developmental processes. We utilized phylogenetic, structural, and biophysical studies to define the interaction networks that facilitate the allosteric mechanism in caspase-3. We show that, within the modified loop, S150 evolved with the apoptotic caspases, while T152 is a more recent evolutionary event in mammalian caspase-3. Substitutions at S150 result in a pH-dependent decrease in dimer stability, and localized changes in the modified loop propagate to the active site of the same protomer through a connecting surface helix. Likewise, a cluster of hydrophobic amino acids connects the conserved loop to the active site of the second protomer. The presence of T152 in the conserved loop introduces a "kill switch" in mammalian caspase-3 while the more ancient S150 reduces without abolishing enzyme activity. These data reveal how evolutionary changes in a conserved allosteric site result in both a common pathway for lowering activity during development as well as introducing a more recent cluster-specific switch to abolish activity.


    Organizational Affiliation

    NC State University, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-3 subunit p17
A
175Homo sapiensGene Names: CASP3 (CPP32)
EC: 3.4.22.56
Find proteins for P42574 (Homo sapiens)
Go to Gene View: CASP3
Go to UniProtKB:  P42574
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Caspase-3 subunit p12
B
102Homo sapiensGene Names: CASP3 (CPP32)
EC: 3.4.22.56
Find proteins for P42574 (Homo sapiens)
Go to Gene View: CASP3
Go to UniProtKB:  P42574
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Acetyl-Asp-Glu-Val-Asp-CMK
C
6N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
A, B
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000238
Query on PRD_000238
CAc-Asp-Glu-Val-Asp-CMKPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.938 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.753α = 90.00
b = 84.405β = 90.00
c = 96.283γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references