1DF0

Crystal structure of M-Calpain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Also Cited By: 3DF0

  • 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 for ...

    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: 
    • 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.Mol.Biol. 4: 539
    • 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.Mol.Biol. 4: 532
    • 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.,Sect.D 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M-CALPAIN
A
700Rattus norvegicusGene Names: Capn2
EC: 3.4.22.53
Find proteins for Q07009 (Rattus norvegicus)
Go to UniProtKB:  Q07009
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CALPAIN
B
184Rattus norvegicusGene Names: Capns1 (Capn4, Css1)
Find proteins for Q64537 (Rattus norvegicus)
Go to UniProtKB:  Q64537
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.696α = 60.37
b = 80.181β = 70.85
c = 80.720γ = 79.49
Software Package:
Software NamePurpose
SHARPphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-05-09
    Type: Structure summary