PDBsum entry: 1kfx

Hydrolase

PDB-id: 1kfx

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

640 a.a. *

176 a.a. *

Waters ×244

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1kfx

Name:

Hydrolase

Title:

Crystal structure of human m-calpain form i

Structure:

M-calpain large subunit. Chain: l. Fragment: catalytic subunit. Synonym: calpain 2, large [catalytic] subunit. Calcium- activated neutral proteinase. Canp. Engineered: yes. M-calpain small subunit. Chain: s. Fragment: regulatory subunit.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_taxid: 7108

Biological unit:

Dimer (from PQS)

UniProt:

Chain L: P17655 (CAN2_HUMAN)

Seq:
Struc:
	Seq:
	Struc:
Seq:		700 a.a.
Struc:		640 a.a.*

Chain S: P04632 (CPNS1_HUMAN)

Seq:

268 a.a.

Struc:

176 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme class:

Chain L: E.C.3.4.22.53   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Cofactor:

Calcium

Resolution:

3.15Å

R-factor:

0.243

R-free:

0.318

Authors:

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

Key ref:

S.Strobl et al. (2000). The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium.. Proc Natl Acad Sci U S A, 97, 588-592. [PubMed id: 10639123] [DOI: 10.1073/pnas.97.2.588]

Date:

23-Nov-01

Release date:

07-Dec-01

Related entries:

1kfu
form ii of m-calpain

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1073/pnas.97.2.588

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

PubMed id: 10639123

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

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

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 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.

Selected figure(s)

Figure 1.
Fig. 1. Ribbon structure of human m-calpain in the absence of calcium, shown in reference orientation. The 80-kDa L-chain starts in the molecular center (green, dI), folds into the surface of the dIIa subdomain (gold, I II linker), forms the papain-like left-side part of the catalytic domain dII (gold, dIIa) and the right-side barrel-like subdomain dIIb (red), descends through the open II III loop (red), builds domain dIII (blue), runs down (magenta, III IV), and forms the right-side calmodulin-like domain dIV (yellow). The 30-kDa S-chain becomes visible from Thr95S onwards (magenta, dV) before forming the left-side calmodulin domain dVI (orange). The catalytic residues Cys105L, His262L, and Asn286L together with Trp106L, Pro287L, and Trp288L (top) are shown with all non-hydrogen atoms. The figure was made with SETOR (34).

Figure 3.
Fig. 3. Superposition of the m-calpain catalytic domain and papain. The papain-like part of the catalytic domain (gold, dIIa) and the barrel-like subdomain dIIb (red) are superimposed with papain (18) (blue) after optimal fit of the left-side papain half to the helical subdomain dIIa. The active site residues Cys105L, His262L, and Asn286L, and Pro287L, Trp288L, and Trp106L are shown in full structure. This "standard view" of papain-like cysteine proteinases (18) is obtained from Fig. 1 by a 90° rotation around a horizontal axis. The figure was made with SETOR (34).

Figures were selected by the author.