1DF0

Crystal structure of M-Calpain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation.

Hosfield, C.M.Elce, J.S.Davies, P.L.Jia, Z.

(1999) EMBO J 18: 6880-6889

  • DOI: 10.1093/emboj/18.24.6880
  • Primary Citation of Related Structures:  
    1DF0

  • PubMed Abstract: 
  • The combination of thiol protease activity and calmodulin-like EF-hands is a feature unique to the calpains. The regulatory mechanisms governing calpain activity are complex, and the nature of the Ca(2+)-induced switch between inactive and active forms has remained elusive in the absence of structural information ...

    The combination of thiol protease activity and calmodulin-like EF-hands is a feature unique to the calpains. The regulatory mechanisms governing calpain activity are complex, and the nature of the Ca(2+)-induced switch between inactive and active forms has remained elusive in the absence of structural information. We describe here the 2.6 A crystal structure of m-calpain in the Ca(2+)-free form, which illustrates the structural basis for the inactivity of calpain in the absence of Ca(2+). It also reveals an unusual thiol protease fold, which is associated with Ca(2+)-binding domains through heterodimerization and a C(2)-like beta-sandwich domain. Strikingly, the structure shows that the catalytic triad is not assembled, indicating that Ca(2+)-binding must induce conformational changes that re-orient the protease domains to form a functional active site. The alpha-helical N-terminal anchor of the catalytic subunit does not occupy the active site but inhibits its assembly and regulates Ca(2+)-sensitivity through association with the regulatory subunit. This Ca(2+)-dependent activation mechanism is clearly distinct from those of classical proteases.


    Related Citations: 
    • Structure of a Calpain Ca(2+)-Binding Domain Reveals a Novel EF-Hand and Ca(2+) -Induced Conformational Changes
      Blanchard, H., Grochulski, P., Li, Y., Arthur, J.S.C., Davies, P.L., Elce, J.S., Cygler, M.
      (1997) Nat Struct Biol 4: 532
    • Crystal Structure of Calcium Bound Domain VI of Calpain at 1.9 A Resolution and its Role in Enzyme Assembly, Regulation, and Inhibitor Binding
      Lin, G.D., Chattopadhyay, D., Maki, M., Wang, K.K., Carson, M., Jin, L., Hatanaka, M., Takano, E., Narayana, S.V.
      (1997) Nat Struct Biol 4: 539
    • Crystallization and X-Ray Crystallographic Analysis of M-Calpain: A Ca2+- Dependent Protease
      Hosfield, C.M., Ye, Q., Arthur, J.S.C., Hegadorn, C., Croall, D.E., Elce, J.S., Jia, Z.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 1484

    Organizational Affiliation

    Department of Biochemistry, Queen's University and The Protein Engineering Network of Centres of Excellence, Kingston, Ontario, Canada K7L 3N6.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
M-CALPAINA700Rattus norvegicusMutation(s): 1 
Gene Names: Capn2
EC: 3.4.22.53
UniProt
Find proteins for Q07009 (Rattus norvegicus)
Explore Q07009 
Go to UniProtKB:  Q07009
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CALPAINB184Rattus norvegicusMutation(s): 0 
Gene Names: Capns1Capn4Css1
UniProt
Find proteins for Q64537 (Rattus norvegicus)
Explore Q64537 
Go to UniProtKB:  Q64537
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.696α = 60.371
b = 80.181β = 70.848
c = 80.72γ = 79.486
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-05-09
    Changes: Structure summary
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation