5IAK

Caspase 3 V266S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection.

Maciag, J.J.Mackenzie, S.H.Tucker, M.B.Schipper, J.L.Swartz, P.Clark, A.C.

(2016) Proc.Natl.Acad.Sci.USA 113: E6080-E6088

  • DOI: 10.1073/pnas.1603549113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that ...

    The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. The data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection.


    Organizational Affiliation

    Department of Biology, University of Texas at Arlington, Arlington, TX 76019; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695.,Department of Biology, University of Texas at Arlington, Arlington, TX 76019; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695; Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27695 clay.clark@uta.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-3
A
278Homo sapiensMutation(s): 1 
Gene 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
ACE-ASP-GLU-VAL-ASK
B
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000238
Query on PRD_000238
BAc-Asp-Glu-Val-Asp-CMKPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.725α = 90.00
b = 84.485β = 90.00
c = 96.302γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release