PDBsum entry 1nx2

Hydrolase

PDB id: 1nx2

Contents

Protein chain

173 a.a. *

Metals

_CA ×4

Waters ×86

* Residue conservation analysis

PDB id:

1nx2

Name:

Hydrolase

Title:

Calpain domain vi

Structure:

Calcium-dependent protease, small subunit. Chain: a. Fragment: domain vi. Synonym: calpain regulatory subunit, calcium-activated neutral proteinase, canp. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Gene: capns1 or capn4. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

2.20Å R-factor: 0.221 R-free: 0.264

Authors:

B.Todd,D.Moore,C.C.S.Deivanayagam,G.-D.Lin,D.Chattopadhyay,M.Maki, K.K.W.Wang,S.V.L.Narayana

Key ref:

B.Todd et al. (2003). A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor. J Mol Biol, 328, 131-146. PubMed id: 12684003 DOI: 10.1016/S0022-2836(03)00274-2

Date:

07-Feb-03 Release date: 19-Aug-03

Protein chain

P04574  (CPNS1_PIG) -  Calpain small subunit 1 from Sus scrofa

Seq: 266 a.a.

Struc: 173 a.a.

DOI no: 10.1016/S0022-2836(03)00274-2

J Mol Biol 328:131-146 (2003)

PubMed id: 12684003

A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.

B.Todd, D.Moore, C.C.Deivanayagam, G.D.Lin, D.Chattopadhyay, M.Maki, K.K.Wang, S.V.Narayana.

ABSTRACT

The Ca(2+)-dependent cysteine protease calpain along with its endogenous inhibitor calpastatin is widely distributed. The interactions between calpain and calpastatin have been studied to better understand the nature of calpain inhibition by calpastatin, which can aid the design of small molecule inhibitors to calpain. Here we present the crystal structure of a complex between a calpastatin peptide and the calcium-binding domain VI of calpain. DIC19 is a 19 residue peptide, which corresponds to one of the three interacting domains of calpastatin, which is known to interact with domain VI of calpain. We present two crystal structures of DIC19 bound to domain VI of calpain, determined by molecular replacement methods to 2.5A and 2.2A resolution. In the process of crystallizing the inhibitor complex, a new native crystal form was identified which had the homodimer 2-fold axis along a crystallographic axis as opposed to the previously observed dimer in the asymmetric unit. The crystal structures of the native domain VI and its inhibitor PD150606 (3-(4-iodophenyl)-2-mercapto-(Z)-2-propenoic acid) complex were determined with the help of molecular replacement methods to 2.0A and 2.3A resolution, respectively. In addition, we built a homology model for the complex between domain IV and DIA19 peptide of calpastatin. Finally, we present a model for the calpastatin-inhibited calpain.

Selected figure(s)

Figure 2.
Figure 2. Ribbon representation of the domain VI crystal structure. (a) Stereographic Ribbon diagrams of the domain VI monomer present in the asymmetric unit. The bound calcium atoms are represented as silver colored spheres. Helices are labeled according to their EF-hand numbering ranging from EF1 to EF5, respectively. The bound DIC19 peptide in helical conformation is represented in yellow and the "mysterious peptide" appeared in the same location as observed in ALG-2 crystal structure[52.] is presented in purple. (b) Ribbon representation of the DVI dimer, depicting interactions through the crystallographic 2-fold axis.

Figure 5.
Figure 5. Stereo view of the surface plots of the hydrophobic inhibitor binding sites. (a) The DIC19 binding region in calcium-bound DVI. DIC19, represented as a helical segment, yellow in color, clearly displays its amphipathic nature with its bulky hydrophobic side-chains buried deep into DVI and polar residues exposed to the solvent (side-chains removed for clarity). (b) Bulky hydrophobic ring of the inhibitor PD150606 and Phe610 of DIC19 occupy the same region of DVI. However, the hydrophobic region that accommodates these inhibitor molecules seems to be flexible enough, varying in size to accommodate different sized inhibitors. c) View of the inhibitor binding regions in the calcium-free DVI structure. DIC19 is positioned in the same place, as in previous Figures, indicating the narrowness of the hydrophobic region.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 328, 131-146) copyright 2003.

Figures were selected by an automated process.