PDBsum entry 1tl9

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Hydrolase/hydrolase inhibitor PDB id
Protein chain
321 a.a. *
_CA ×2
Waters ×287
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: High resolution crystal structure of calpain i protease core complex with leupeptin
Structure: Calpain 1, large [catalytic] subunit. Chain: a. Fragment: residues 27-356. Synonym: calcium-activated neutral proteinase, canp, mu-typ micromolar-calpain. Engineered: yes. Leupeptin inhibitor. Chain: b. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: capn1, cls1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.217     R-free:   0.244
Authors: T.Moldoveanu,R.L.Campbell,D.Cuerrier,P.L.Davies
Key ref:
T.Moldoveanu et al. (2004). Crystal structures of calpain-E64 and -leupeptin inhibitor complexes reveal mobile loops gating the active site. J Mol Biol, 343, 1313-1326. PubMed id: 15491615 DOI: 10.1016/j.jmb.2004.09.016
09-Jun-04     Release date:   02-Nov-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P97571  (CAN1_RAT) -  Calpain-1 catalytic subunit
713 a.a.
321 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Calpain-1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Cofactor: Ca(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     calcium ion binding     2 terms  


DOI no: 10.1016/j.jmb.2004.09.016 J Mol Biol 343:1313-1326 (2004)
PubMed id: 15491615  
Crystal structures of calpain-E64 and -leupeptin inhibitor complexes reveal mobile loops gating the active site.
T.Moldoveanu, R.L.Campbell, D.Cuerrier, P.L.Davies.
The endogenous calpain inhibitor, calpastatin, modulates some patho-physiological aspects of calpain signaling. Excess calpain can escape this inhibition and as well, many calpain isoforms and autolytically generated protease core fragments are not inhibited by calpastatin. There is a need, therefore, to develop specific, cell-permeable calpain inhibitors to block uncontrolled proteolysis and prevent tissue damage during brain and heart ischemia, spinal-cord injury and Alzheimer's diseases. Here, we report the first high-resolution crystal structures of rat mu-calpain protease core complexed with two traditional, low molecular mass inhibitors, leupeptin and E64. These structures show that access to a slightly deeper, but otherwise papain-like active site is gated by two flexible loops. These loops are divergent among the calpain isoforms giving a potential structural basis for substrate/inhibitor selectivity over other papain-like cysteine proteases and between members of the calpain family.
  Selected figure(s)  
Figure 4.
Figure 4. Close-up of µI-II-inhibitor interactions. Stereoview of the interactions between leupeptin (green) and E64 (magenta) with calpain µI-II. Residues within domains I and II are colored blue and cyan, respectively. The residues found within 4 Å of leupeptin and E64 are colored by atom type (carbon, yellow; oxygen, red; nitrogen, blue; and sulfur, orange). Hydrogen-bonding interactions are indicated by dotted blue lines. (A) and (B) Surface and stick representations of the calpain µI-II-leupeptin complex. (C) and (D) Stick and surface representations of the calpain µI-II-E64 complex.
Figure 7.
Figure 7. Comparison of calpain's active site with that of papain and cathepsins K and B. (A) Calpain µI-II-leupeptin complex. (B) Papain-leupeptin complex (PDB code 1POP). (C)-(F) Close-up views of active site cleft (rotated about 90° from (A) and (B)). (C) Calpain µI-II-leupeptin. (D) Papain-leupeptin. (E) Cathepsin K-E64 (PDB code 1ATK). (F) Cathepsin B-benzyloxycarbonyl-Arg-Ser(O-Bzl) chloromethylketone (PDB code 1THE45).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 1313-1326) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20555428 J.S.Gilchrist, T.Cook, B.Abrenica, B.Rashidkhani, and G.N.Pierce (2010).
Extensive autolytic fragmentation of membranous versus cytosolic calpain following myocardial ischemia-reperfusion.
  Can J Physiol Pharmacol, 88, 584-594.  
18037508 C.Palermo, and J.A.Joyce (2008).
Cysteine cathepsin proteases as pharmacological targets in cancer.
  Trends Pharmacol Sci, 29, 22-28.  
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.  
18694642 I.O.Donkor, and R.Korukonda (2008).
Synthesis and calpain inhibitory activity of peptidomimetic compounds with constrained amino acids at the P2 position.
  Bioorg Med Chem Lett, 18, 4806-4808.  
18702462 J.Qian, D.Cuerrier, P.L.Davies, Z.Li, J.C.Powers, and R.L.Campbell (2008).
Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions.
  J Med Chem, 51, 5264-5270.
PDB codes: 2r9c 2r9f
18348880 M.Azuma, and T.R.Shearer (2008).
The role of calcium-activated protease calpain in experimental retinal pathology.
  Surv Ophthalmol, 53, 150-163.  
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
17218315 D.Cuerrier, T.Moldoveanu, R.L.Campbell, J.Kelly, B.Yoruk, S.H.Verhelst, D.Greenbaum, M.Bogyo, and P.L.Davies (2007).
Development of calpain-specific inactivators by screening of positional scanning epoxide libraries.
  J Biol Chem, 282, 9600-9611.
PDB codes: 2nqg 2nqi
17608959 D.E.Croall, and K.Ersfeld (2007).
The calpains: modular designs and functional diversity.
  Genome Biol, 8, 218.  
17135258 M.Averna, R.Stifanese, R.De Tullio, M.Passalacqua, E.Defranchi, F.Salamino, E.Melloni, and S.Pontremoli (2007).
Regulation of calpain activity in rat brain with altered Ca2+ homeostasis.
  J Biol Chem, 282, 2656-2665.  
16623703 M.Averna, R.Stifanese, R.De Tullio, E.Defranchi, F.Salamino, E.Melloni, and S.Pontremoli (2006).
Interaction between catalytically inactive calpain and calpastatin. Evidence for its occurrence in stimulated cells.
  FEBS J, 273, 1660-1668.  
16216885 D.Cuerrier, T.Moldoveanu, and P.L.Davies (2005).
Determination of peptide substrate specificity for mu-calpain by a peptide library-based approach: the importance of primed side interactions.
  J Biol Chem, 280, 40632-40641.  
16125114 M.Bartoli, and I.Richard (2005).
Calpains in muscle wasting.
  Int J Biochem Cell Biol, 37, 2115-2133.  
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 codes are shown on the right.