spacer
spacer

PDBsum entry 3df0

Go to PDB code: 
protein metals Protein-protein interface(s) links
Hydrolase PDB id
3df0
Jmol
Contents
Protein chains
676 a.a. *
174 a.a. *
56 a.a. *
Metals
_CA ×10
* Residue conservation analysis
PDB id:
3df0
Name: Hydrolase
Title: Calcium-dependent complex between m-calpain and 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 87-270.
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: capn2. Expressed in: escherichia coli. Gene: capns1, capn4, css1. Gene: cast.
Resolution:
2.95Å     R-factor:   0.232     R-free:   0.299
Authors: T.Moldoveanu,K.Gehring,D.R.Green
Key ref:
T.Moldoveanu et al. (2008). Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains. Nature, 456, 404-408. PubMed id: 19020622 DOI: 10.1038/nature07353
Date:
11-Jun-08     Release date:   11-Nov-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q07009  (CAN2_RAT) -  Calpain-2 catalytic subunit
Seq:
Struc:
 
Seq:
Struc:
700 a.a.
676 a.a.*
Protein chain
Pfam   ArchSchema ?
Q64537  (CPNS1_RAT) -  Calpain small subunit 1
Seq:
Struc:
270 a.a.
174 a.a.
Protein chain
Pfam   ArchSchema ?
P27321  (ICAL_RAT) -  Calpastatin
Seq:
Struc:
 
Seq:
Struc:
713 a.a.
56 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.3.4.22.53  - 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/nature07353 Nature 456:404-408 (2008)
PubMed id: 19020622  
 
 
Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains.
T.Moldoveanu, K.Gehring, D.R.Green.
 
  ABSTRACT  
 
The Ca(2+)-dependent cysteine proteases, calpains, regulate cell migration, cell death, insulin secretion, synaptic function and muscle homeostasis. Their endogenous inhibitor, calpastatin, consists of four inhibitory repeats, each of which neutralizes an activated calpain with exquisite specificity and potency. Despite the physiological importance of this interaction, the structural basis of calpain inhibition by calpastatin is unknown. Here we report the 3.0 A structure of Ca(2+)-bound m-calpain in complex with the first calpastatin repeat, both from rat, revealing the mechanism of exclusive specificity. The structure highlights the complexity of calpain activation by Ca(2+), illustrating key residues in a peripheral domain that serve to stabilize the protease core on Ca(2+) binding. Fully activated calpain binds ten Ca(2+) atoms, resulting in several conformational changes allowing recognition by calpastatin. Calpain inhibition is mediated by the intimate contact with three critical regions of calpastatin. Two regions target the penta-EF-hand domains of calpain and the third occupies the substrate-binding cleft, projecting a loop around the active site thiol to evade proteolysis.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Complex between Ca^2+-bound m-calpain and calpastatin. a, Overall structure shows regions A, B and C of calpastatin bound to DIV, DI–III and DVI of calpain, respectively. The intervening sequences of calpastatin are devoid of electron density (red dots). The central part of the inhibitory region B forms the occluding loop at the active site. The active site in the protease core DI–II is stabilized by DIII. Calpain heterodimerization is largely defined at the DIV–DVI interface. Alternate conformations at the interface between the DI–III core and the DIV–DVI heterodimer (black dots) are possible^30. b, ^15N,^1H-HSQC (heteronuclear single quantum correlation) spectrum of the complex between ^13C,^15N-labelled calpastatin (residues 128–226, Supplementary Fig. 2b) and unlabelled calpain identified flexible/disordered residues of calpastatin. Connected sample strips from the HNCA NMR experiment are inset.
Figure 4.
Figure 4: Calpain–calpastatin proteolytic system. A schematic diagram illustrating the Ca^2+-induced activation of calpain and its inhibition by calpastatin. DIII has a fundamental role in relaying the Ca^2+-induced structural changes (red dotted arrows) from the peripheral domains to the catalytically competent yet labile protease core. Concerted binding of the intrinsically unstructured protein (IUP) calpastatin to peripheral domains and the active site of calpain results in low-nanomolar inhibition.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 456, 404-408) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20694146 A.de Morrée, D.Lutje Hulsik, A.Impagliazzo, H.H.van Haagen, P.de Galan, A.van Remoortere, P.A.'t Hoen, G.B.van Ommen, R.R.Frants, and S.M.van der Maarel (2010).
Calpain 3 is a rapid-action, unidirectional proteolytic switch central to muscle remodeling.
  PLoS One, 5, e11940.  
21053238 C.J.Farady, and C.S.Craik (2010).
Mechanisms of macromolecular protease inhibitors.
  Chembiochem, 11, 2341-2346.  
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.  
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.  
20007729 Z.Dosztányi, B.Mészáros, and I.Simon (2010).
Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins.
  Brief Bioinform, 11, 225-243.  
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.