Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

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

Macromolecule Content

• Total Structure Weight: 71.63 kDa 
• Atom Count: 3907 
• Residue Count: 474 
• Unique protein chains: 3

4ZVR

Caspase-7 Variant 4 (V4) with reprogrammed substrate specificity due to Y230V/W232Y/S234V/Q276D substitutions bound to DEVD inhibitor.

• DOI: 10.2210/pdb4ZVR/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-05-18 Released: 2016-04-20 
• Deposition Author(s): Hill, M.E., MacPherson, D.J., Hardy, J.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.224 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Reprogramming Caspase-7 Specificity by Regio-Specific Mutations and Selection Provides Alternate Solutions for Substrate Recognition.

Hill, M.E., MacPherson, D.J., Wu, P., Julien, O., Wells, J.A., Hardy, J.A.

(2016) ACS Chem Biol 11: 1603-1612

• PubMed: 27032039 
• DOI: 10.1021/acschembio.5b00971
• Primary Citation of Related Structures:  
  4ZVO, 4ZVP, 4ZVQ, 4ZVR, 4ZVS, 4ZVT, 4ZVU


• PubMed Abstract: 
  

The ability to routinely engineer protease specificity can allow us to better understand and modulate their biology for expanded therapeutic and industrial applications. Here, we report a new approach based on a caged green fluorescent protein (CA-GFP) reporter that allows for flow-cytometry-based selection in bacteria or other cell types enabling selection of intracellular protease specificity, regardless of the compositional complexity of the protease. Here, we apply this approach to introduce the specificity of caspase-6 into caspase-7, an intracellular cysteine protease important in cellular remodeling and cell death. We found that substitution of substrate-contacting residues from caspase-6 into caspase-7 was ineffective, yielding an inactive enzyme, whereas saturation mutagenesis at these positions and selection by directed evolution produced active caspases. The process produced a number of nonobvious mutations that enabled conversion of the caspase-7 specificity to match caspase-6. The structures of the evolved-specificity caspase-7 (esCasp-7) revealed alternate binding modes for the substrate, including reorganization of an active site loop. Profiling the entire human proteome of esCasp-7 by N-terminomics demonstrated that the global specificity toward natural protein substrates is remarkably similar to that of caspase-6. Because the esCasp-7 maintained the core of caspase-7, we were able to identify a caspase-6 substrate, lamin C, that we predict relies on an exosite for substrate recognition. These reprogrammed proteases may be the first tool built with the express intent of distinguishing exosite dependent or independent substrates. This approach to specificity reprogramming should also be generalizable across a wide range of proteases.

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Organizational Affiliation: 

Department of Chemistry, 104 LGRT, 710 N. Pleasant St., University of Massachusetts , Amherst, Massachusetts 01003, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7	A, C	198	Homo sapiens	Mutation(s): 0  Gene Names: CASP7, MCH3 EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens) Explore P55210  Go to UniProtKB:  P55210
NIH Common Fund Data Resources
PHAROS:  P55210 GTEx:  ENSG00000165806

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7	B, D	113	Homo sapiens	Mutation(s): 4  Gene Names: CASP7, MCH3 EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens) Explore P55210  Go to UniProtKB:  P55210
NIH Common Fund Data Resources
PHAROS:  P55210 GTEx:  ENSG00000165806

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide ACE-ASP-GLU-VAL-ASJ	E, F	5	synthetic construct	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000422	E, F	Ac-Asp-Glu-Val-Asp-Aldehyde	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.224 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.98	α = 90
b = 87.98	β = 90
c = 187.311	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
iMOSFLM	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-05-18 
• Released Date: 2016-04-20 
Deposition Author(s): Hill, M.E., MacPherson, D.J., Hardy, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM080532

Revision History 

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2016-07-06
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence