PDBsum entry: 1kxr

Hydrolase

PDB-id: 1kxr

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Description

Header details

Header records

References

PROCHECK

Protein chains

320 a.a. *

Metal ions

_CA ×4

Waters ×359

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1kxr

Name:

Hydrolase

Title:

Crystal structure of calcium-bound protease core of calpain i

Structure:

Thiol protease domains i and ii. Chain: a, b. Fragment: residues 27-356. Synonym: calpain i protease core. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: capn1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

UniProt:

Chains A, B: P97571 (CAN1_RAT)

Seq:

Struc:

Seq:

Struc:

Seq:

713 a.a.

Struc:

320 a.a.*

Key:

PfamA domain

Secondary structure

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

Enzyme class:

E.C.3.4.22.52   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Cofactor:

Calcium

Resolution:

2.07Å

R-factor:

0.213

R-free:

0.256

Authors:

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

Key ref:

T.Moldoveanu et al. (2002). A Ca(2+) switch aligns the active site of calpain.. Cell, 108, 649-660. [PubMed id: 11893336] [DOI: 10.1016/S0092-8674(02)00659-1]

Date:

01-Feb-02

Release date:

20-Mar-02

Related entries:

1df0
crystal structure of rat calcium-free calpain ii heterodime
1kfu
crystal structure of calcium-free human calpain ii
heterodimer - crystal form i
1kfx
crystal structure of calcium-free human calpain ii
heterodimer - crystal form ii
1dvi
crystal structure of calcium-bound domain vi homodimer
... plus others (see Header records)

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Clefts

Surface

Key reference

DOI no: 10.1016/S0092-8674(02)00659-1

Cell 108:649-660 (2002)

PubMed id: 11893336

A Ca(2+) switch aligns the active site of calpain.

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

ABSTRACT

Ca(2+) signaling by calpains leads to controlled proteolysis during processes ranging from cytoskeleton remodeling in mammals to sex determination in nematodes. Deregulated Ca(2+) levels result in aberrant proteolysis by calpains, which contributes to tissue damage in heart and brain ischemias as well as neurodegeneration in Alzheimer's disease. Here we show that activation of the protease core of mu calpain requires cooperative binding of two Ca(2+) atoms at two non-EF-hand sites revealed in the 2.1 A crystal structure. Conservation of the Ca(2+) binding residues defines an ancestral general mechanism of activation for most calpain isoforms, including some that lack EF-hand domains. The protease region is not affected by the endogenous inhibitor, calpastatin, and may contribute to calpain-mediated pathologies when the core is released by autoproteolysis.

Selected figure(s)

Figure 4.
Figure 4. Ca^2+-Induced Conformational Changes in the Active Site Region of Calpain and Proposed Activation Mechanism(A) DI and II of inactive human m calpain (Strobl et al., 2000). The ribbon presentation is colored pink, with the side chains of three critical residues (equivalent to μ R104, W298, and E333) colored orange. DI and II are rotated 5° relative to each other, and C105 and H262 are 10.5 Å apart.(B) DI of μI-II (blue) was overlapped onto DI from m calpain (pink) using the program Align (Cohen, 1997). The gold sphere indicates the Ca^2+ ion.(C) Exposure of the Ca^2+ binding site in DII (cyan) resulting from attraction of the E333 side chain by R104 from DI.(D) R104-E333 double salt bridge stereo view.(E) Overlap of DII from μI-II (cyan) onto DII from m calpain (pink) showing the loops that coordinate the second Ca^2+. Note: a discrepancy in the m calpain structure around G295 results in a discontinuity in that peptide loop.(F) Stereo view of the hydrophobic pocket formed by Ca^2+ binding to DII.(G) Ca^2+ bound μI-II, showing the arrangement of the Ca^2+ ions relative to the active site cleft. This is a 90° rotation of the view in Figure 2A.

Figure 6.
Figure 6. Regulation of Heterodimeric Calpain by Ca^2+A generic model for Ca^2+ bound calpain was constructed by substituting the Ca^2+ bound structure of DI-II into the human m calpain heterodimer (Strobl et al., 2000) while overlapping DIV and VI with the Ca^2+ bound DVI heterodimer structure (Blanchard et al., 1997). DII was positioned to optimize DIII interactions. The anchor peptide (red helix) was placed in the Ca^2+-free conformation where it interacts with DVI (gray). Two consecutive yet cooperative levels of Ca^2+ regulation are proposed, both acting on a different segment of the circularized structure. Stage 1 includes anchor release (Nakagawa et al., 2001), shown by the red dotted arrow. As well, under certain conditions small subunit dissociation (Pal et al., 2001) and the potential binding of Ca^2+ to DIII (Hosfield et al. 2001 and Tompa et al. 2001) may help free the protease region from constraints. Stage 2 is active site assembly (black dotted arrows) as seen in μI-II. It follows the onset of stage 1 but may also influence it if the tendency to realign the active site pulls against the restraint. Ca^2+ ions are colored gold (seen in X-ray structures) or red (postulated or confirmed by mutagenesis; Dutt et al., 2000). Transparent spheres in DIV and VI are Ca^2+ at EF-4 sites that are likely filled only at high CaCl[2] (>20 mM) concentrations. Calpain association with membranes (double gray lines) may also contribute to activation (as reviewed in Nakagawa et al., 2001).

The above figures are reprinted by permission from Cell Press: Cell (2002, 108, 649-660) copyright 2002.

Figures were selected by an automated process.