3EDR

The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.231 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for executioner caspase recognition of P5 position in substrates.

Fu, G.Chumanevich, A.A.Agniswamy, J.Fang, B.Harrison, R.W.Weber, I.T.

(2008) Apoptosis 13: 1291-1302

  • DOI: https://doi.org/10.1007/s10495-008-0259-9
  • Primary Citation of Related Structures:  
    3EDQ, 3EDR

  • PubMed Abstract: 

    Caspase-3, -6 and -7 cleave many proteins at specific sites to induce apoptosis. Their recognition of the P5 position in substrates has been investigated by kinetics, modeling and crystallography. Caspase-3 and -6 recognize P5 in pentapeptides as shown by enzyme activity data and interactions observed in the crystal structure of caspase-3/LDESD and in a model for caspase-6. In caspase-3 the P5 main-chain was anchored by interactions with Ser209 in loop-3 and the P5 Leu side-chain interacted with Phe250 and Phe252 in loop-4 consistent with 50% increased hydrolysis of LDEVD relative to DEVD. Caspase-6 formed similar interactions and showed a preference for polar P5 in QDEVD likely due to interactions with polar Lys265 and hydrophobic Phe263 in loop-4. Caspase-7 exhibited no preference for P5 residue in agreement with the absence of P5 interactions in the caspase-7/LDESD crystal structure. Initiator caspase-8, with Pro in the P5-anchoring position and no loop-4, had only 20% activity on tested pentapeptides relative to DEVD. Therefore, caspases-3 and -6 bind P5 using critical loop-3 anchoring Ser/Thr and loop-4 side-chain interactions, while caspase-7 and -8 lack P5-binding residues.


  • Organizational Affiliation

    Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-7
A, C
173Homo sapiensMutation(s): 0 
Gene Names: CASP7MCH3
EC: 3.4.22.60
UniProt & NIH Common Fund Data Resources
Find proteins for P55210 (Homo sapiens)
Explore P55210 
Go to UniProtKB:  P55210
PHAROS:  P55210
GTEx:  ENSG00000165806 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55210
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-7
B, D
97Homo sapiensMutation(s): 0 
Gene Names: CASP7MCH3
EC: 3.4.22.60
UniProt & NIH Common Fund Data Resources
Find proteins for P55210 (Homo sapiens)
Explore P55210 
Go to UniProtKB:  P55210
PHAROS:  P55210
GTEx:  ENSG00000165806 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55210
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor Ac-ldesd-cho peptide
E, F
6Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36114 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36114 
Go to UniProtKB:  P36114
Entity Groups  
UniProt GroupP36114
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.231 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.637α = 90
b = 88.637β = 90
c = 187.708γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2013-02-27
    Changes: Other
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection