5IC6

Crystal structure of caspase-7 DEVE peptide complex

DOI: 10.2210/pdb5IC6/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-02-22 Released: 2016-07-20
Deposition Author(s): Seaman, J.E., Julien, O., Lee, P.S., Rettenmaier, T.J., Thomsen, N.D., Wells, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.241
R-Value Work: 0.197
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 27367566 Search on PubMedSearch on PubMed Central
DOI: 10.1038/cdd.2016.62
Primary Citation of Related Structures:
5IC4, 5IC6

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 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

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7 subunit p20	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
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Reference Sequence

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(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7 subunit p11	B, D	113	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
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DEVE peptide	E, F	4	synthetic construct	Mutation(s): 0
Protein Feature View Expand
Reference Sequence