5IC4

Crystal structure of caspase-3 DEVE peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cacidases: caspases can cleave after aspartate, glutamate and phosphoserine residues.

Seaman, J.E.Julien, O.Lee, P.S.Rettenmaier, T.J.Thomsen, N.D.Wells, J.A.

(2016) Cell Death Differ. 23: 1717-1726

  • DOI: 10.1038/cdd.2016.62
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Caspases are a family of proteases found in all metazoans, including a dozen in humans, that drive the terminal stages of apoptosis as well as other cellular remodeling and inflammatory events. Caspases are named because they are cysteine class enzym ...

    Caspases are a family of proteases found in all metazoans, including a dozen in humans, that drive the terminal stages of apoptosis as well as other cellular remodeling and inflammatory events. Caspases are named because they are cysteine class enzymes shown to cleave after aspartate residues. In the past decade, we and others have developed unbiased proteomic methods that collectively identified ~2000 native proteins cleaved during apoptosis after the signature aspartate residues. Here, we explore non-aspartate cleavage events and identify 100s of substrates cleaved after glutamate in both human and murine apoptotic samples. The extended consensus sequence patterns are virtually identical for the aspartate and glutamate cleavage sites suggesting they are cleaved by the same caspases. Detailed kinetic analyses of the dominant apoptotic executioner caspases-3 and -7 show that synthetic substrates containing DEVD↓ are cleaved only twofold faster than DEVE↓, which is well within the 500-fold range of rates that natural proteins are cut. X-ray crystallography studies confirm that the two acidic substrates bind in virtually the same way to either caspases-3 or -7 with minimal adjustments to accommodate the larger glutamate. Lastly, during apoptosis we found 121 proteins cleaved after serine residues that have been previously annotated to be phosphorylation sites. We found that caspase-3, but not caspase-7, can cleave peptides containing DEVpS↓ at only threefold slower rate than DEVD↓, but does not cleave the unphosphorylated serine peptide. There are only a handful of previously reported examples of proteins cleaved after glutamate and none after phosphorserine. Our studies reveal a much greater promiscuity for cleaving after acidic residues and the name 'cacidase' could aptly reflect this broader specificity.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-3 subunit p17
A, C, E, G
175Homo sapiensMutation(s): 0 
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
Caspase-3 subunit p12
B, D, F, H
107Homo sapiensMutation(s): 0 
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: 3
MoleculeChainsSequence LengthOrganismDetails
DEVE peptide
I, J, K, L
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MKE
Query on MKE
I, J, K, L
NON-POLYMERC6 H11 N O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 133.820α = 90.00
b = 177.796β = 90.00
c = 193.430γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR21 CA186007
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM081051
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM097316
National Institutes of Health/National Cancer InstituteUnited StatesR01 CA154802
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM007175
National Institutes of Health/National Cancer InstituteUnited StatesF31 CA180378

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations