3H1P

Mature Caspase-7 I213A with DEVD-CHO inhibitor bound to active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

L2' loop is critical for caspase-7 active site formation.

Witkowski, W.A.Hardy, J.A.

(2009) Protein Sci. 18: 1459-1468

  • DOI: 10.1002/pro.151

  • PubMed Abstract: 
  • The active sites of caspases are composed of four mobile loops. A loop (L2) from one half of the dimer interacts with a loop (L2') from the other half of the dimer to bind substrate. In an inactive form, the two L2' loops form a cross-dimer hydrogen- ...

    The active sites of caspases are composed of four mobile loops. A loop (L2) from one half of the dimer interacts with a loop (L2') from the other half of the dimer to bind substrate. In an inactive form, the two L2' loops form a cross-dimer hydrogen-bond network over the dimer interface. Although the L2' loop has been implicated as playing a central role in the formation of the active-site loop bundle, its precise role in catalysis has not been shown. A detailed understanding of the active and inactive conformations is essential to control the caspase function. We have interrogated the contributions of the residues in the L2' loop to catalytic function and enzyme stability. In wild-type and all mutants, active-site binding results in substantial stabilization of the complex. One mutation, P214A, is significantly destabilized in the ligand-free conformation, but is as stable as wild type when bound to substrate, indicating that caspase-7 rests in different conformations in the absence and presence of substrate. Residues K212 and I213 in the L2' loop are shown to be essential for substrate-binding and thus proper catalytic function of the caspase. In the crystal structure of I213A, the void created by side-chain deletion is compensated for by rearrangement of tyrosine 211 to fill the void, suggesting that the requirements of substrate-binding are sufficiently strong to induce the active conformation. Thus, although the L2' loop makes no direct contacts with substrate, it is essential for buttressing the substrate-binding groove and is central to native catalytic efficiency.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-7
A, B
260Homo sapiensMutation(s): 1 
Gene Names: CASP7 (MCH3)
EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens)
Go to Gene View: CASP7
Go to UniProtKB:  P55210
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N-ACETYL-L-ALPHA-ASPARTYL-L-ALPHA-GLUTAMYL-N-[(2S)-1-CARBOXY-3-HYDROXYPROPAN-2-YL]-L-VALINAMIDE
C, D
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000422
Query on PRD_000422
C,DAc-Asp-Glu-Val-Asp-AldehydePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.347α = 90.00
b = 89.347β = 90.00
c = 186.101γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CrystalCleardata collection
PDB_EXTRACTdata extraction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2011-10-05
    Type: Structure summary
  • Version 1.3: 2013-02-27
    Type: Other
  • Version 1.4: 2017-11-01
    Type: Refinement description