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PDBsum entry 1nx1

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protein metals Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
1nx1
Jmol
Contents
Protein chains
173 a.a. *
11 a.a. *
Metals
_CA ×8
Waters ×104
* Residue conservation analysis
PDB id:
1nx1
Name: Hydrolase/hydrolase inhibitor
Title: Calpain domain vi complexed with calpastatin inhibitory doma
Structure: Calcium-dependent protease, small subunit. Chain: a, b. Fragment: domain vi. Synonym: calpain regulatory subunit, calcium-activated neut proteinase, canp. Engineered: yes. Calpastatin. Chain: c, d. Fragment: dic, residues 230-240.
Source: Sus scrofa. Pig. Organism_taxid: 9823. Gene: capns1 or capn4. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.208     R-free:   0.253
Authors: B.Todd,D.Moore,C.C.S.Deivanayagam,G.-D.Lin,D.Chattopadhyay,M 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04574  (CPNS1_PIG) -  Calpain small subunit 1
Seq:
Struc:
266 a.a.
173 a.a.
Protein chains
Pfam   ArchSchema ?
P12675  (ICAL_PIG) -  Calpastatin
Seq:
Struc:
 
Seq:
Struc:
713 a.a.
11 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     calcium ion binding     1 term  

 

 
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.  

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.  
19349622 A.Drewniak, B.J.van Raam, J.Geissler, A.T.Tool, O.R.Mook, T.K.van den Berg, F.Baas, and T.W.Kuijpers (2009).
Changes in gene expression of granulocytes during in vivo granulocyte colony-stimulating factor/dexamethasone mobilization for transfusion purposes.
  Blood, 113, 5979-5998.  
  21099278 J.D.Johnson, K.Otani, G.I.Bell, and K.S.Polonsky (2009).
Impaired insulin secretion in transgenic mice over-expressing calpastatin in pancreatic β-cells.
  Islets, 1, 242-248.  
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.  
18793761 D.E.Croall, L.M.Vanhooser, and R.E.Cashon (2008).
Detecting the active conformation of calpain with calpastatin-based reagents.
  Biochim Biophys Acta, 1784, 1676-1686.  
18095873 J.Pfizer, I.Assfalg-Machleidt, W.Machleidt, and N.Schaschke (2008).
Inhibition of human mu-calpain by conformationally constrained calpastatin peptides.
  Biol Chem, 389, 83-90.  
19020623 R.A.Hanna, R.L.Campbell, and P.L.Davies (2008).
Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin.
  Nature, 456, 409-412.
PDB code: 3bow
19020622 T.Moldoveanu, K.Gehring, and D.R.Green (2008).
Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains.
  Nature, 456, 404-408.
PDB code: 3df0
17608959 D.E.Croall, and K.Ersfeld (2007).
The calpains: modular designs and functional diversity.
  Genome Biol, 8, 218.  
17359359 I.M.Medana, N.P.Day, T.T.Hien, N.T.Mai, D.Bethell, N.H.Phu, G.D.Turner, J.Farrar, N.J.White, and M.M.Esiri (2007).
Cerebral calpain in fatal falciparum malaria.
  Neuropathol Appl Neurobiol, 33, 179-192.  
15613629 M.Bokor, V.Csizmók, D.Kovács, P.Bánki, P.Friedrich, P.Tompa, and K.Tompa (2005).
NMR relaxation studies on the hydrate layer of intrinsically unstructured proteins.
  Biophys J, 88, 2030-2037.  
15255177 A.Wendt, V.F.Thompson, and D.E.Goll (2004).
Interaction of calpastatin with calpain: a review.
  Biol Chem, 385, 465-472.  
15073171 B.G.Diaz, T.Moldoveanu, M.J.Kuiper, R.L.Campbell, and P.L.Davies (2004).
Insertion sequence 1 of muscle-specific calpain, p94, acts as an internal propeptide.
  J Biol Chem, 279, 27656-27666.  
15366927 L.Subramanian, J.W.Crabb, J.Cox, I.Durussel, T.M.Walker, P.R.van Ginkel, S.Bhattacharya, J.M.Dellaria, K.Palczewski, and A.S.Polans (2004).
Ca2+ binding to EF hands 1 and 3 is essential for the interaction of apoptosis-linked gene-2 with Alix/AIP1 in ocular melanoma.
  Biochemistry, 43, 11175-11186.  
14594950 Y.Ono, K.Kakinuma, F.Torii, A.Irie, K.Nakagawa, S.Labeit, K.Abe, K.Suzuki, and H.Sorimachi (2004).
Possible regulation of the conventional calpain system by skeletal muscle-specific calpain, p94/calpain 3.
  J Biol Chem, 279, 2761-2771.  
12857354 D.Mitchell, and A.Bell (2003).
PEST sequences in the malaria parasite Plasmodium falciparum: a genomic study.
  Malar J, 2, 16.  
14500891 Z.Mucsi, F.Hudecz, M.Hollósi, P.Tompa, and P.Friedrich (2003).
Binding-induced folding transitions in calpastatin subdomains A and C.
  Protein Sci, 12, 2327-2336.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.