1KFU

Crystal Structure of Human m-Calpain Form II

DOI: 10.2210/pdb1KFU/pdb
Entry: 1KFU supersedes: 1DKV

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2001-11-23 Released: 2001-12-07
Deposition Author(s): Strobl, S., Fernandez-Catalan, C., Braun, M., Huber, R., Masumoto, H., Nakagawa, K., Irie, A., Sorimachi, H., Bourenkow, G., Bartunik, H., Suzuki, K., Bode, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.276
R-Value Work: 0.221

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium.

Strobl, S., Fernandez-Catalan, C., Braun, M., Huber, R., Masumoto, H., Nakagawa, K., Irie, A., Sorimachi, H., Bourenkow, G., Bartunik, H., Suzuki, K., Bode, W.

(2000) Proc Natl Acad Sci U S A 97: 588-592

PubMed: 10639123 Search on PubMedSearch on PubMed Central
DOI: 10.1073/pnas.97.2.588
Primary Citation of Related Structures:
1KFX, 1KFU

PubMed Abstract:

Calpains (calcium-dependent cytoplasmic cysteine proteinases) are implicated in processes such as cytoskeleton remodeling and signal transduction. The 2.3-A crystal structure of full-length heterodimeric [80-kDa (dI-dIV) + 30-kDa (dV+dVI)] human m-calpain crystallized in the absence of calcium reveals an oval disc-like shape, with the papain-like catalytic domain dII and the two calmodulin-like domains dIV+dVI occupying opposite poles, and the tumor necrosis factor alpha-like beta-sandwich domain dIII and the N-terminal segments dI+dV located between. Compared with papain, the two subdomains dIIa+dIIb of the catalytic unit are rotated against one another by 50 degrees, disrupting the active site and the substrate binding site, explaining the inactivity of calpains in the absence of calcium. Calcium binding to an extremely negatively charged loop of domain dIII (an electrostatic switch) could release the adjacent barrel-like subdomain dIIb to move toward the helical subdomain dIIa, allowing formation of a functional catalytic center. This switch loop could also mediate membrane binding, thereby explaining calpains' strongly reduced calcium requirements in vivo. The activity status at the catalytic center might be further modulated by calcium binding to the calmodulin domains via the N-terminal linkers.

Related Citations:

Crystallization and preliminary X-ray analysis of recombinant full-length m-calpain
Masumoto, H., Nakagawa, K., Irie, S., Sorimachi, H., Suzuki, K., Bourenkow, G., Bartunik, H., Fernandez-Catalan, C., Bode, W., Strobl, S.
(2000) Acta Crystallogr D Biol Crystallogr 56: 73

Structural basis for possible calcium-induced activation mechanisms of calpains
Reverter, D., Strobl, S., Fernandez-Catalan, C., Sorimachi, H., Suzuki, K., Bode, W.
(2001) Biol Chem 382: 753

The structure of calcium-free human m-calpain
Reverter, D., Sorimachi, H., Bode, W.
(2001) Trends Cardiovasc Med 11: 222

Organizational Affiliation:

Max-Planck-Institute of Biochemistry, Am Klopferspitz 18a, D 82 152 Planegg-Martinsried, Germany.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M-CALPAIN LARGE SUBUNIT	L	699	Homo sapiens	Mutation(s): 0 Gene Names: CAPN2, CANPL2 EC: 3.4.22.53
Find proteins for P17655 (Homo sapiens) Explore P17655 Go to UniProtKB: P17655
NIH Common Fund Data Resources
PHAROS: P17655 GTEx: ENSG00000162909
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M-CALPAIN SMALL SUBUNIT	S	184	Homo sapiens	Mutation(s): 0 Gene Names: CAPNS1, CAPN4, CAPNS
Find proteins for P04632 (Homo sapiens) Explore P04632 Go to UniProtKB: P04632
NIH Common Fund Data Resources
PHAROS: P04632 GTEx: ENSG00000126247
Protein Feature View Expand
Reference Sequence