Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 137.01 kDa 
• Atom Count: 6781 
• Modelled Residue Count: 886 
• Deposited Residue Count: 1196 
• Unique protein chains: 1

4FXO

Zinc-mediated allosteric inhibiton of caspase-6

• DOI: 10.2210/pdb4FXO/pdb

• Classification: apoptosis, HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-03 Released: 2012-08-22 
• Deposition Author(s): Velazquez-Delgado, E.M., Hardy, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.233 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

Literature

Zinc-mediated Allosteric Inhibition of Caspase-6.

Velazquez-Delgado, E.M., Hardy, J.A.

(2012) J Biol Chem 287: 36000-36011

• PubMed: 22891250 
• DOI: 10.1074/jbc.M112.397752
• Primary Citation of Related Structures:  
  4FXO


• PubMed Abstract: 
  

Zinc and caspase-6 have independently been implicated in several neurodegenerative disorders. Depletion of zinc intracellularly leads to apoptosis by an unknown mechanism. Zinc inhibits cysteine proteases, including the apoptotic caspases, leading to the hypothesis that zinc-mediated inhibition of caspase-6 might contribute to its regulation in a neurodegenerative context. Using inductively coupled plasma optical emission spectroscopy, we observed that caspase-6 binds one zinc per monomer, under the same conditions where the zinc leads to complete loss of enzymatic activity. To understand the molecular details of zinc binding and inhibition, we performed an anomalous diffraction experiment above the zinc edge. The anomalous difference maps showed strong 5σ peaks, indicating the presence of one zinc/monomer bound at an exosite distal from the active site. Zinc was not observed bound to the active site. The zinc in the exosite was liganded by Lys-36, Glu-244, and His-287 with a water molecule serving as the fourth ligand, forming a distorted tetrahedral ligation sphere. This exosite appears to be unique to caspase-6, as the residues involved in zinc binding were not conserved across the caspase family. Our data suggest that binding of zinc at the exosite is the primary route of inhibition, potentially locking caspase-6 into the inactive helical conformation.

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Organizational Affiliation: 

Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-6	A, B, C, D	299	Homo sapiens	Mutation(s): 0  Gene Names: CASP6, MCH2 EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens) Explore P55212  Go to UniProtKB:  P55212
NIH Common Fund Data Resources
PHAROS:  P55212 GTEx:  ENSG00000138794

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.233 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.696	α = 90
b = 90.855	β = 90.3
c = 85.763	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-03 
• Released Date: 2012-08-22 
Deposition Author(s): Velazquez-Delgado, E.M., Hardy, J.A.

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2012-09-05
  Changes: Database references
• Version 1.2: 2012-11-07
  Changes: Database references