1SC1

Crystal structure of an active-site ligand-free form of the human caspase-1 C285A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of a ligand-free and malonate-bound human caspase-1: implications for the mechanism of substrate binding.

Romanowski, M.J.Scheer, J.M.O'Brien, T.McDowell, R.S.

(2004) Structure 12: 1361-1371

  • DOI: 10.1016/j.str.2004.05.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Caspase-1, a mediator of the posttranslational processing of IL-1beta and IL-18, requires an aspartic acid in the P1 position of its substrates. The mechanisms of caspase-1 activation remain poorly understood despite numerous structures of the enzyme ...

    Caspase-1, a mediator of the posttranslational processing of IL-1beta and IL-18, requires an aspartic acid in the P1 position of its substrates. The mechanisms of caspase-1 activation remain poorly understood despite numerous structures of the enzyme complexed with aspartate-based inhibitors. Here we report a crystal structure of ligand-free caspase-1 that displays dramatic rearrangements of loops defining the active site to generate a closed conformation that is incompatible with substrate binding. A structure of the enzyme complexed with malonate shows the protein in its open (active-site ligand-bound) conformation in which malonate reproduces the hydrogen bonding network observed in structures with covalent inhibitors. These results illustrate the essential function of the obligatory aspartate recognition element that opens the active site of caspase-1 to substrates and may be the determinant responsible for the conformational changes between ligand-free and -bound forms of the enzyme, and suggest a new approach for identifying novel aspartic acid mimetics.


    Organizational Affiliation

    Department of Structural Biology, Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, California 94080, USA. romanom@sunesis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 beta convertase
A
178Homo sapiensMutation(s): 1 
Gene Names: CASP1 (IL1BC, IL1BCE)
EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens)
Go to Gene View: CASP1
Go to UniProtKB:  P29466
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 beta convertase
B
88Homo sapiensMutation(s): 0 
Gene Names: CASP1 (IL1BC, IL1BCE)
EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens)
Go to Gene View: CASP1
Go to UniProtKB:  P29466
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.231 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.782α = 90.00
b = 71.782β = 90.00
c = 118.451γ = 120.00
Software Package:
Software NamePurpose
d*TREKdata scaling
CrystalCleardata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance