Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29212.59 
• Atom Count: 2035 
• Residue Count: 256 
• Unique protein chains: 2

4QTY

Caspase-3 E190A

• DOI: 10.2210/pdb4QTY/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2014-07-09 Released: 2014-11-05 
• Deposition Author(s): Cade, C., Swartz, P.D., MacKenzie, S.H., Clark, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.602 Å
• R-Value Free: 0.195 
• R-Value Work: 0.167 

Literature

Modifying caspase-3 activity by altering allosteric networks.

Cade, C., Swartz, P., MacKenzie, S.H., Clark, A.C.

(2014) Biochemistry 53: 7582-7595

• PubMed: 25343534 
• DOI: 10.1021/bi500874k
• Primary Citation of Related Structures:  
  4QUL, 4QUJ, 4QUI, 4QUH, 4QUG, 4QUE, 4QUD, 4QUB, 4QUA, 4QU9, 4QU8, 4QU5, 4QU0, 4QTX


• PubMed Abstract: 
  

Caspases have several allosteric sites that bind small molecules or peptides. Allosteric regulators are known to affect caspase enzyme activity, in general, by facilitating large conformational changes that convert the active enzyme to a zymogen-like form in which the substrate-binding pocket is disordered. Mutations in presumed allosteric networks also decrease activity, although large structural changes are not observed. Mutation of the central V266 to histidine in the dimer interface of caspase-3 inactivates the enzyme by introducing steric clashes that may ultimately affect positioning of a helix on the protein surface. The helix is thought to connect several residues in the active site to the allosteric dimer interface. In contrast to the effects of small molecule allosteric regulators, the substrate-binding pocket is intact in the mutant, yet the enzyme is inactive. We have examined the putative allosteric network, in particular the role of helix 3, by mutating several residues in the network. We relieved steric clashes in the context of caspase-3(V266H), and we show that activity is restored, particularly when the restorative mutation is close to H266. We also mimicked the V266H mutant by introducing steric clashes elsewhere in the allosteric network, generating several mutants with reduced activity. Overall, the data show that the caspase-3 native ensemble includes the canonical active state as well as an inactive conformation characterized by an intact substrate-binding pocket, but with an altered helix 3. The enzyme activity reflects the relative population of each species in the native ensemble.

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Organizational Affiliation: 

Department of Molecular and Structural Biochemistry and ‡Center for Comparative Medicine and Translational Research, North Carolina State University , Raleigh, North Carolina 27695, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Caspase-3	A	250	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR	F	6	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
AZI	A	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000238	F	Ac-Asp-Glu-Val-Asp-CMK	Peptide-like / Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.602 Å
• R-Value Free: 0.195 
• R-Value Work: 0.167 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 69.215	α = 90.00
b = 84.830	β = 90.00
c = 96.349	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
SCALEPACK	data scaling
SERGUI	data collection
DENZO	data reduction
PHENIX	phasing
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-09 
• Released Date: 2014-11-05 
• Deposition Author(s): Cade, C., Swartz, P.D., MacKenzie, S.H., Clark, A.C.

Revision History 

• Version 1.0: 2014-11-05
  Type: Initial release
• Version 1.1: 2014-12-24
  Type: Database references
• Version 1.2: 2017-11-22
  Type: Refinement description