PDBsum entry: 1mdw

Hydrolase

PDB id: 1mdw

Contents

Protein chains

319 a.a. *

Metals

_CA ×4

Waters ×365

* Residue conservation analysis

PDB id:

1mdw

Name:

Hydrolase

Title:

Crystal structure of calcium-bound protease core of calpain ii reveals the basis for intrinsic inactivation

Structure:

Calpain ii, catalytic subunit. Chain: a, b. Fragment: protease core domains i and ii (residues 17-346). Synonym: calcium-activated neutral proteinase, canp, m- type, m-calpain, millimolar-calpain. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: calpain ii. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.95Å R-factor: 0.207 R-free: 0.243

Authors:

T.Moldoveanu,C.M.Hosfield,D.Lim,Z.Jia,P.L.Davies

Key ref:

T.Moldoveanu et al. (2003). Calpain silencing by a reversible intrinsic mechanism. Nat Struct Biol, 10, 371-378. PubMed id: 12665854 DOI: 10.1038/nsb917

Date:

07-Aug-02 Release date: 29-Apr-03

Protein chains

Q07009  (CAN2_RAT) -  Calpain-2 catalytic subunit

Seq: 700 a.a.

Struc: 319 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.22.53 - Calpain-2.
• Cofactor: Calcium

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: proteolysis (1 term)
• Biochemical function: calcium-dependent cysteine-type endopeptidase activity (1 term)

DOI no: 10.1038/nsb917

Nat Struct Biol 10:371-378 (2003)

PubMed id: 12665854

Calpain silencing by a reversible intrinsic mechanism.

T.Moldoveanu, C.M.Hosfield, D.Lim, Z.Jia, P.L.Davies.

ABSTRACT

Uncontrolled activation of calpain can lead to necrotic cell death and irreversible tissue damage. We have discovered an intrinsic mechanism whereby the autolysis-generated protease core fragment of calpain is inactivated through the inherent instability of a key alpha-helix. This auto-inactivation state was captured by the 1.9 A Ca(2+)-bound structure of the protease core from m-calpain, and sequence alignments suggest that it applies to about half of the calpain isoforms. Intact calpain large subunits are also subject to this inhibition, which can be prevented through assembly of the heterodimers. Other isoforms or their released cores are not silenced by this mechanism and might contribute to calpain patho-physiologies.

Selected figure(s)

Figure 2.
Figure 2. Structural comparison of the calcium-bound - and m-minicalpains. a, Overlap of mI-II onto I-II using ALIGN30. Gold spheres indicate Ca^2+ ions. The protease core of mI-II (red/pink) is superimposed on I-II (transparent blue/cyan). -strands and -helices are numbered sequentially from the N terminus (N) to the C terminus (C). The side chain atoms of the catalytic triad residues are colored in red (oxygen), dark blue (nitrogen) and gray (carbon), and the bonds have the domain color. b, Stereo view of the mI-II region showing oxygen coordinations to DI Ca^2+ (eight) and DII Ca^2+ (pentagonal bipyramid), as well as the double salt bridge between Arg94 and Glu323. Side chains are structured exactly as predicted from the Ca^2+-bound I-II structure.

Figure 4.
Figure 4. Hydrophobic core collapses in mI-II but not in I-II. The hydrophobic core stabilized by helix 7 is shown for the two minicalpains. The color scheme is the same as that in Fig. 2, with Phe207/217 and Trp106/116 shown in green and pink, respectively. a, Stereo view of mI-II core. The helix-breaking Gly 203 is orange. b, Stereo view of the I-II core. The peptide 207 -213 (yellow ribbon) is structured in I-II because Ala 213 (orange) stabilizes helix 7.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 371-378) copyright 2003.

Figures were selected by an automated process.