PDBsum entry 3bow

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protein metals Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
Protein chains
680 a.a. *
174 a.a. *
65 a.a. *
_CA ×10
Waters ×176
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Structure of m-calpain in complex with calpastatin
Structure: Calpain-2 catalytic subunit. Chain: a. Synonym: calpain-2 large subunit, calcium-activated neutral proteinase 2, canp 2, calpain m-type, m-calpain, millimolar engineered: yes. Mutation: yes. Calpain small subunit 1. Chain: b. Fragment: unp residues 88-270.
Source: Rattus norvegicus. Brown rat,rat,rats. Organism_taxid: 10116. Gene: capn2. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: capns1, capn4, css1. Gene: cast.
2.40Å     R-factor:   0.201     R-free:   0.258
Authors: R.A.Hanna,R.L.Campbell,P.L.Davies
Key ref:
R.A.Hanna et al. (2008). Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin. Nature, 456, 409-412. PubMed id: 19020623 DOI: 10.1038/nature07451
17-Dec-07     Release date:   25-Nov-08    
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Protein chain
Pfam   ArchSchema ?
Q07009  (CAN2_RAT) -  Calpain-2 catalytic subunit
700 a.a.
680 a.a.*
Protein chain
Pfam   ArchSchema ?
Q64537  (CPNS1_RAT) -  Calpain small subunit 1
270 a.a.
174 a.a.
Protein chain
Pfam   ArchSchema ?
P27321  (ICAL_RAT) -  Calpastatin
713 a.a.
65 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - Calpain-2.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Cofactor: Ca(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     perinuclear endoplasmic reticulum   15 terms 
  Biological process     cellular response to amino acid stimulus   7 terms 
  Biochemical function     protein binding     9 terms  


DOI no: 10.1038/nature07451 Nature 456:409-412 (2008)
PubMed id: 19020623  
Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin.
R.A.Hanna, R.L.Campbell, P.L.Davies.
Calpains are non-lysosomal calcium-dependent cysteine proteinases that selectively cleave proteins in response to calcium signals and thereby control cellular functions such as cytoskeletal remodelling, cell cycle progression, gene expression and apoptotic cell death. In mammals, the two best-characterized members of the calpain family, calpain 1 and calpain 2 (micro-calpain and m-calpain, respectively), are ubiquitously expressed. The activity of calpains is tightly controlled by the endogenous inhibitor calpastatin, which is an intrinsically unstructured protein capable of reversibly binding and inhibiting four molecules of calpain, but only in the presence of calcium. To date, the mechanism of inhibition by calpastatin and the basis for its absolute specificity have remained speculative. It was not clear how this unstructured protein inhibits calpains without being cleaved itself, nor was it known how calcium induced changes that facilitated the binding of calpastatin to calpain. Here we report the 2.4-A-resolution crystal structure of the calcium-bound calpain 2 heterodimer bound by one of the four inhibitory domains of calpastatin. Calpastatin is seen to inhibit calpain by occupying both sides of the active site cleft. Although the inhibitor passes through the active site cleft it escapes cleavage in a novel manner by looping out and around the active site cysteine. The inhibitory domain of calpastatin recognizes multiple lower affinity sites present only in the calcium-bound form of the enzyme, resulting in an interaction that is tight, specific and calcium dependent. This crystal structure, and that of a related complex, also reveal the conformational changes that calpain undergoes on binding calcium, which include opening of the active site cleft and movement of the domains relative to each other to produce a more compact enzyme.
  Selected figure(s)  
Figure 1.
Figure 1: Overview of calpastatin domain 4 (CAST4) bound to calpain 2. The overall structure of CAST4 (purple) bound to the inactive C105S mutant of calpain 2. CAST4, which is unstructured in the absence of calpain, forms three -helices when in complex with the enzyme. Helices in subdomains A and C, which are in contact with DIV (yellow) and DVI (orange), and the helix in subdomain B, which is in contact with the protease core DI and DII (blue and light blue, respectively) are shown in ribbon representation. DIII is coloured green. Gaps in the electron density of CAST4 are indicated by missing residues between D589 and K594, and between N629 and P652.
Figure 2.
Figure 2: Specific interactions of calpastatin with calpain entering and leaving the active-site cleft. a–d, The 27-residue B-peptide^7 is coloured as follows: the residues that make the loop out of the active site are coloured yellow, the residues N-terminal to the loop are purple, and the residues C-terminal to the loop are green. Other calpastatin residues are coloured dark grey. Hydrogen-bond interactions of calpastatin with calpain (coloured as in Fig. 1) are shown by black dashed lines. O and N atoms are coloured red and blue, respectively. a, Overview of calpain binding at the active site of calpain. b, Close-up view of the calpastatin at the unprimed side of the active site. c, Close-up view of calpastatin looping away from the catalytic residue. d, Close-up view of calpastatin at the primed side of the active site.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 456, 409-412) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21520072 C.Y.Lin, T.S.Lee, C.C.Chen, C.A.Chang, Y.J.Lin, Y.P.Hsu, and L.T.Ho (2011).
Endothelin-1 exacerbates lipid accumulation by increasing the protein degradation of the ATP-binding cassette transporter G1 in macrophages.
  J Cell Physiol, 226, 2198-2205.  
21149284 F.Paquet-Durand, S.Beck, S.Michalakis, T.Goldmann, G.Huber, R.Mühlfriedel, D.Trifunović, M.D.Fischer, E.Fahl, G.Duetsch, E.Becirovic, U.Wolfrum, T.van Veen, M.Biel, N.Tanimoto, and M.W.Seeliger (2011).
A key role for cyclic nucleotide gated (CNG) channels in cGMP-related retinitis pigmentosa.
  Hum Mol Genet, 20, 941-947.  
21434837 I.O.Donkor (2011).
Calpain inhibitors: a survey of compounds reported in the patent and scientific literature.
  Expert Opin Ther Pat, 21, 601-636.  
21508973 S.J.Storr, N.O.Carragher, M.C.Frame, T.Parr, and S.G.Martin (2011).
The calpain system and cancer.
  Nat Rev Cancer, 11, 364-374.  
21173228 S.K.Tyagarajan, H.Ghosh, G.E.Yévenes, I.Nikonenko, C.Ebeling, C.Schwerdel, C.Sidler, H.U.Zeilhofer, B.Gerrits, D.Muller, and J.M.Fritschy (2011).
Regulation of GABAergic synapse formation and plasticity by GSK3beta-dependent phosphorylation of gephyrin.
  Proc Natl Acad Sci U S A, 108, 379-384.  
21053238 C.J.Farady, and C.S.Craik (2010).
Mechanisms of macromolecular protease inhibitors.
  Chembiochem, 11, 2341-2346.  
20223856 D.J.Macqueen, M.L.Delbridge, S.Manthri, and I.A.Johnston (2010).
A newly classified vertebrate calpain protease, directly ancestral to CAPN1 and 2, episodically evolved a restricted physiological function in placental mammals.
  Mol Biol Evol, 27, 1886-1902.  
21030783 H.Sorimachi, S.Hata, and Y.Ono (2010).
Expanding members and roles of the calpain superfamily and their genetically modified animals.
  Exp Anim, 59, 549-566.  
21209906 J.L.Fuentes, M.S.Strayer, and A.G.Matera (2010).
Molecular determinants of survival motor neuron (SMN) protein cleavage by the calcium-activated protease, calpain.
  PLoS One, 5, e15769.  
20233039 M.Montal (2010).
Botulinum neurotoxin: a marvel of protein design.
  Annu Rev Biochem, 79, 591-617.  
20460380 Y.Ono, K.Ojima, F.Torii, E.Takaya, N.Doi, K.Nakagawa, S.Hata, K.Abe, and H.Sorimachi (2010).
Skeletal muscle-specific calpain is an intracellular Na+-dependent protease.
  J Biol Chem, 285, 22986-22998.  
20849418 Y.Osako, Y.Maemoto, R.Tanaka, H.Suzuki, H.Shibata, and M.Maki (2010).
Autolytic activity of human calpain 7 is enhanced by ESCRT-III-related protein IST1 through MIT-MIM interaction.
  FEBS J, 277, 4412-4426.  
19712109 A.Trümpler, B.Schlott, P.Herrlich, P.A.Greer, and F.D.Böhmer (2009).
Calpain-mediated degradation of reversibly oxidized protein-tyrosine phosphatase 1B.
  FEBS J, 276, 5622-5633.  
19378261 O.Toke, Z.Bánóczi, G.Tárkányi, P.Friedrich, and F.Hudecz (2009).
Folding transitions in calpain activator peptides studied by solution NMR spectroscopy.
  J Pept Sci, 15, 404-410.  
19342550 R.Chandramohanadas, P.H.Davis, D.P.Beiting, M.B.Harbut, C.Darling, G.Velmourougane, M.Y.Lee, P.A.Greer, D.S.Roos, and D.C.Greenbaum (2009).
Apicomplexan parasites co-opt host calpains to facilitate their escape from infected cells.
  Science, 324, 794-797.  
19285946 S.A.Woodcock, C.Rooney, M.Liontos, Y.Connolly, V.Zoumpourlis, A.D.Whetton, V.G.Gorgoulis, and A.Malliri (2009).
SRC-induced disassembly of adherens junctions requires localized phosphorylation and degradation of the rac activator tiam1.
  Mol Cell, 33, 639-653.  
19020611 R.L.Mellgren (2008).
Structural biology: Enzyme knocked for a loop.
  Nature, 456, 337-338.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.