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PDBsum entry 1kfu

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protein Protein-protein interface(s) links
Hydrolase PDB id
1kfu
Jmol
Contents
Protein chains
699 a.a. *
184 a.a. *
Waters ×411
* Residue conservation analysis
PDB id:
1kfu
Name: Hydrolase
Title: Crystal structure of human m-calpain form ii
Structure: M-calpain large subunit. Chain: l. Fragment: catalytic subunit. Synonym: calpain 2, large [catalytic] subunit. Calcium-acti neutral proteinase. Canp. Engineered: yes. M-calpain small subunit. Chain: s. Fragment: regulatory subunit.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_taxid: 7108
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.221     R-free:   0.276
Authors: S.Strobl,C.Fernandez-Catalan,M.Braun,R.Huber,H.Masumoto,K.Na A.Irie,H.Sorimachi,G.Bourenkow,H.Bartunik,K.Suzuki,W.Bode
Key ref:
S.Strobl et al. (2000). The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium. Proc Natl Acad Sci U S A, 97, 588-592. PubMed id: 10639123 DOI: 10.1073/pnas.97.2.588
Date:
23-Nov-01     Release date:   07-Dec-01    
Supersedes: 1dkv
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17655  (CAN2_HUMAN) -  Calpain-2 catalytic subunit
Seq:
Struc:
 
Seq:
Struc:
700 a.a.
699 a.a.*
Protein chain
Pfam   ArchSchema ?
P04632  (CPNS1_HUMAN) -  Calpain small subunit 1
Seq:
Struc:
268 a.a.
184 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain L: 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   16 terms 
  Biological process     cellular response to amino acid stimulus   8 terms 
  Biochemical function     protein binding     9 terms  

 

 
DOI no: 10.1073/pnas.97.2.588 Proc Natl Acad Sci U S A 97:588-592 (2000)
PubMed id: 10639123  
 
 
The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium.
S.Strobl, C.Fernandez-Catalan, M.Braun, R.Huber, H.Masumoto, K.Nakagawa, A.Irie, H.Sorimachi, G.Bourenkow, H.Bartunik, K.Suzuki, W.Bode.
 
  ABSTRACT  
 
Calpains (calcium-dependent cytoplasmic cysteine proteinases) are implicated in processes such as cytoskeleton remodeling and signal transduction. The 2.3-A crystal structure of full-length heterodimeric [80-kDa (dI-dIV) + 30-kDa human m-calpain crystallized in the absence of calcium reveals an oval disc-like shape, with the papain-like catalytic domain dII and the two calmodulin-like domains dIV+dVI occupying opposite poles, and the tumor necrosis factor alpha-like beta-sandwich domain dIII and the N-terminal segments dI+dV located between. Compared with papain, the two subdomains dIIa+dIIb of the catalytic unit are rotated against one another by 50 degrees, disrupting the active site and the substrate binding site, explaining the inactivity of calpains in the absence of calcium. Calcium binding to an extremely negatively charged loop of domain dIII (an electrostatic switch) could release the adjacent barrel-like subdomain dIIb to move toward the helical subdomain dIIa, allowing formation of a functional catalytic center. This switch loop could also mediate membrane binding, thereby explaining calpains' strongly reduced calcium requirements in vivo. The activity status at the catalytic center might be further modulated by calcium binding to the calmodulin domains via the N-terminal linkers.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Ribbon structure of human m-calpain in the absence of calcium, shown in reference orientation. The 80-kDa L-chain starts in the molecular center (green, dI), folds into the surface of the dIIa subdomain (gold, I II linker), forms the papain-like left-side part of the catalytic domain dII (gold, dIIa) and the right-side barrel-like subdomain dIIb (red), descends through the open II III loop (red), builds domain dIII (blue), runs down (magenta, III IV), and forms the right-side calmodulin-like domain dIV (yellow). The 30-kDa S-chain becomes visible from Thr95S onwards (magenta, dV) before forming the left-side calmodulin domain dVI (orange). The catalytic residues Cys105L, His262L, and Asn286L together with Trp106L, Pro287L, and Trp288L (top) are shown with all non-hydrogen atoms. The figure was made with SETOR (34).
Figure 3.
Fig. 3. Superposition of the m-calpain catalytic domain and papain. The papain-like part of the catalytic domain (gold, dIIa) and the barrel-like subdomain dIIb (red) are superimposed with papain (18) (blue) after optimal fit of the left-side papain half to the helical subdomain dIIa. The active site residues Cys105L, His262L, and Asn286L, and Pro287L, Trp288L, and Trp106L are shown in full structure. This "standard view" of papain-like cysteine proteinases (18) is obtained from Fig. 1 by a 90° rotation around a horizontal axis. The figure was made with SETOR (34).
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21458141 G.Shanmugam, N.Phambu, and P.L.Polavarapu (2011).
Unusual structural transition of antimicrobial VP1 peptide.
  Biophys Chem, 155, 104-108.  
  21338355 K.Sato, S.Minegishi, J.Takano, F.Plattner, T.Saito, A.Asada, H.Kawahara, N.Iwata, T.C.Saido, and S.Hisanaga (2011).
Calpastatin, an endogenous calpain-inhibitor protein, regulates the cleavage of the Cdk5 activator p35 to p25.
  J Neurochem, 117, 504-515.  
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.  
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.  
19723289 A.I.Arroba, D.Wallace, A.Mackey, E.J.de la Rosa, and T.G.Cotter (2009).
IGF-I maintains calpastatin expression and attenuates apoptosis in several models of photoreceptor cell death.
  Eur J Neurosci, 30, 975-986.  
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.  
19239622 I.Russo, A.Oksman, and D.E.Goldberg (2009).
Fatty acid acylation regulates trafficking of the unusual Plasmodium falciparum calpain to the nucleolus.
  Mol Microbiol, 72, 229-245.  
19909374 S.Hailfinger, F.Rebeaud, and M.Thome (2009).
Adapter and enzymatic functions of proteases in T-cell activation.
  Immunol Rev, 232, 334-347.  
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.  
18672675 L.A.Bondareva, and N.N.Nemova (2008).
[Molecular evolution of intracellular Ca2+-dependent proteases]
  Bioorg Khim, 34, 295-302.  
18073773 M.B.Bevers, and R.W.Neumar (2008).
Mechanistic role of calpains in postischemic neurodegeneration.
  J Cereb Blood Flow Metab, 28, 655-673.  
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.  
17666040 J.S.Evans, and M.D.Turner (2007).
Emerging functions of the calpain superfamily of cysteine proteases in neuroendocrine secretory pathways.
  J Neurochem, 103, 849-859.  
17210638 K.Tonami, Y.Kurihara, H.Aburatani, Y.Uchijima, T.Asano, and H.Kurihara (2007).
Calpain 6 is involved in microtubule stabilization and cytoskeletal organization.
  Mol Cell Biol, 27, 2548-2561.  
17416893 M.M.Peñas, A.Hervás-Aguilar, T.Múnera-Huertas, E.Reoyo, M.A.Peñalva, H.N.Arst, and J.Tilburn (2007).
Further characterization of the signaling proteolysis step in the Aspergillus nidulans pH signal transduction pathway.
  Eukaryot Cell, 6, 960-970.  
16740134 A.Fernández-Montalván, I.Assfalg-Machleidt, D.Pfeiler, H.Fritz, M.Jochum, and W.Machleidt (2006).
Mu-calpain binds to lipid bilayers via the exposed hydrophobic surface of its Ca2+-activated conformation.
  Biol Chem, 387, 617-627.  
17151322 F.Harris, S.Biswas, J.Singh, S.Dennison, and D.A.Phoenix (2006).
Calpains and their multiple roles in diabetes mellitus.
  Ann N Y Acad Sci, 1084, 452-480.  
16297652 F.Raynaud, R.Fabrice, C.Jond-Necand, J.N.Carole, A.Marcilhac, M.Anne, D.Fürst, F.Dieter, Y.Benyamin, and B.Yves (2006).
Calpain 1-gamma filamin interaction in muscle cells: a possible in situ regulation by PKC-alpha.
  Int J Biochem Cell Biol, 38, 404-413.  
16283653 F.Salamino, R.Minafra, V.Grano, N.Diano, D.G.Mita, S.Pontremoli, and E.Melloni (2006).
Effect of extremely low frequency magnetic fields on calpain activation.
  Bioelectromagnetics, 27, 43-50.  
16927317 J.L.Hood, W.H.Brooks, and T.L.Roszman (2006).
Subcellular mobility of the calpain/calpastatin network: an organelle transient.
  Bioessays, 28, 850-859.  
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.  
16997142 M.E.Saez, R.Ramirez-Lorca, F.J.Moron, and A.Ruiz (2006).
The therapeutic potential of the calpain family: new aspects.
  Drug Discov Today, 11, 917-923.  
16884486 Y.Benyamin (2006).
The structural basis of calpain behavior.
  FEBS J, 273, 3413-3414.  
15885106 F.Raynaud, E.Fernandez, G.Coulis, L.Aubry, X.Vignon, N.Bleimling, M.Gautel, Y.Benyamin, and A.Ouali (2005).
Calpain 1-titin interactions concentrate calpain 1 in the Z-band edges and in the N2-line region within the skeletal myofibril.
  FEBS J, 272, 2578-2590.  
16315106 K.Ersfeld, H.Barraclough, and K.Gull (2005).
Evolutionary relationships and protein domain architecture in an expanded calpain superfamily in kinetoplastid parasites.
  J Mol Evol, 61, 742-757.  
16125114 M.Bartoli, and I.Richard (2005).
Calpains in muscle wasting.
  Int J Biochem Cell Biol, 37, 2115-2133.  
16028216 M.D.Turner, P.G.Cassell, and G.A.Hitman (2005).
Calpain-10: from genome search to function.
  Diabetes Metab Res Rev, 21, 505-514.  
15843151 M.Ghosh, S.Shanker, I.Siwanowicz, K.Mann, W.Machleidt, and T.A.Holak (2005).
Proteolysis of insulin-like growth factor binding proteins (IGFBPs) by calpain.
  Biol Chem, 386, 85-93.  
15930958 M.Ridderstråle, H.Parikh, and L.Groop (2005).
Calpain 10 and type 2 diabetes: are we getting closer to an explanation?
  Curr Opin Clin Nutr Metab Care, 8, 361-366.  
15893952 P.Costelli, P.Reffo, F.Penna, R.Autelli, G.Bonelli, and F.M.Baccino (2005).
Ca(2+)-dependent proteolysis in muscle wasting.
  Int J Biochem Cell Biol, 37, 2134-2146.  
16207081 P.Friedrich, and Z.Bozóky (2005).
Digestive versus regulatory proteases: on calpain action in vivo.
  Biol Chem, 386, 609-612.  
15653743 S.R.Dennison, S.Dante, T.Hauss, K.Brandenburg, F.Harris, and D.A.Phoenix (2005).
Investigations into the membrane interactions of m-calpain domain V.
  Biophys J, 88, 3008-3017.  
14993287 A.Glading, R.J.Bodnar, I.J.Reynolds, H.Shiraha, L.Satish, D.A.Potter, H.C.Blair, and A.Wells (2004).
Epidermal growth factor activates m-calpain (calpain II), at least in part, by extracellular signal-regulated kinase-mediated phosphorylation.
  Mol Cell Biol, 24, 2499-2512.  
15382138 P.Friedrich, P.Tompa, and A.Farkas (2004).
The calpain-system of Drosophila melanogaster: coming of age.
  Bioessays, 26, 1088-1096.  
15102361 S.Biswas, F.Harris, S.Dennison, J.Singh, and D.A.Phoenix (2004).
Calpains: targets of cataract prevention?
  Trends Mol Med, 10, 78-84.  
14749380 T.Franz, L.Winckler, T.Boehm, and T.N.Dear (2004).
Capn5 is expressed in a subset of T cells and is dispensable for development.
  Mol Cell Biol, 24, 1649-1654.  
12857354 D.Mitchell, and A.Bell (2003).
PEST sequences in the malaria parasite Plasmodium falciparum: a genomic study.
  Malar J, 2, 16.  
14579356 E.K.Leinala, J.S.Arthur, P.Grochulski, P.L.Davies, J.S.Elce, and Z.Jia (2003).
A second binding site revealed by C-terminal truncation of calpain small subunit, a penta-EF-hand protein.
  Proteins, 53, 649-655.
PDB code: 1np8
12951515 E.Kimura, K.Abe, K.Suzuki, and H.Sorimachi (2003).
Heterogeneous nuclear ribonucleoprotein K interacts with and is proteolyzed by calpain in vivo.
  Biosci Biotechnol Biochem, 67, 1786-1796.  
14622253 F.Raynaud, C.Bonnal, E.Fernandez, L.Bremaud, M.Cerutti, M.C.Lebart, C.Roustan, A.Ouali, and Y.Benyamin (2003).
The calpain 1-alpha-actinin interaction. Resting complex between the calcium-dependent protease and its target in cytoskeleton.
  Eur J Biochem, 270, 4662-4670.  
14656436 G.P.Pal, T.De Veyra, J.S.Elce, and Z.Jia (2003).
Crystal structure of a micro-like calpain reveals a partially activated conformation with low Ca2+ requirement.
  Structure, 11, 1521-1526.
PDB code: 1qxp
12554956 G.P.Pal, T.DeVeyra, J.S.Elce, and Z.Jia (2003).
Purification, crystallization and preliminary X-ray analysis of a mu-like calpain.
  Acta Crystallogr D Biol Crystallogr, 59, 369-371.  
12843569 H.Sorimachi, and Y.Kawabata (2003).
[Calpain and pathology in view of structure-function relationships]
  Nippon Yakurigaku Zasshi, 122, 21-29.  
12665854 T.Moldoveanu, C.M.Hosfield, D.Lim, Z.Jia, and P.L.Davies (2003).
Calpain silencing by a reversible intrinsic mechanism.
  Nat Struct Biol, 10, 371-378.
PDB code: 1mdw
12517342 W.Iwasaki, H.Sasaki, A.Nakamura, K.Kohama, and M.Tanokura (2003).
Metal-free and Ca2+-bound structures of a multidomain EF-hand protein, CBP40, from the lower eukaryote Physarum polycephalum.
  Structure, 11, 75-85.
PDB codes: 1ij5 1ij6
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.  
11854009 A.Glading, D.A.Lauffenburger, and A.Wells (2002).
Cutting to the chase: calpain proteases in cell motility.
  Trends Cell Biol, 12, 46-54.  
11914728 A.Khorchid, and M.Ikura (2002).
How calpain is activated by calcium.
  Nat Struct Biol, 9, 239-241.  
12437134 D.Reverter, M.Braun, C.Fernandez-Catalan, S.Strobl, H.Sorimachi, and W.Bode (2002).
Flexibility analysis and structure comparison of two crystal forms of calcium-free human m-calpain.
  Biol Chem, 383, 1415-1422.  
11830654 E.Carafoli (2002).
Calcium signaling: a tale for all seasons.
  Proc Natl Acad Sci U S A, 99, 1115-1122.  
  11934353 H.Malina, C.Richter, B.Frueh, and O.M.Hess (2002).
Lens epithelial cell apoptosis and intracellular Ca2+ increase in the presence of xanthurenic acid.
  BMC Ophthalmol, 2, 1.  
11909964 H.Shiraha, A.Glading, J.Chou, Z.Jia, and A.Wells (2002).
Activation of m-calpain (calpain II) by epidermal growth factor is limited by protein kinase A phosphorylation of m-calpain.
  Mol Cell Biol, 22, 2716-2727.  
12423339 K.Brandenburg, F.Harris, S.Dennison, U.Seydel, and D.Phoenix (2002).
Domain V of m-calpain shows the potential to form an oblique-orientated alpha-helix, which may modulate the enzyme's activity via interactions with anionic lipid.
  Eur J Biochem, 269, 5414-5422.  
12379276 N.O.Carragher, and M.C.Frame (2002).
Calpain: a role in cell transformation and migration.
  Int J Biochem Cell Biol, 34, 1539-1543.  
11929961 S.E.Lid, D.Gruis, R.Jung, J.A.Lorentzen, E.Ananiev, M.Chamberlin, X.Niu, R.Meeley, S.Nichols, and O.A.Olsen (2002).
The defective kernel 1 (dek1) gene required for aleurone cell development in the endosperm of maize grains encodes a membrane protein of the calpain gene superfamily.
  Proc Natl Acad Sci U S A, 99, 5460-5465.  
11258679 B.G.Díaz, S.Gross, I.Assfalg-Machleidt, D.Pfeiler, N.Gollmitzer, D.Gabrijelcic-Geiger, M.T.Stubbs, H.Fritz, E.A.Auerswald, and W.Machleidt (2001).
Cystatins as calpain inhibitors: engineered chicken cystatin- and stefin B-kininogen domain 2 hybrids support a cystatin-like mode of interaction with the catalytic subunit of mu-calpain.
  Biol Chem, 382, 97.  
11843187 D.Gabrijelcic-Geiger, R.Mentele, B.Meisel, H.Hinz, I.Assfalg-Machleidt, W.Machleidt, A.Möller, and E.A.Auerswald (2001).
Human micro-calpain: simple isolation from erythrocytes and characterization of autolysis fragments.
  Biol Chem, 382, 1733-1737.  
11517928 D.Reverter, S.Strobl, C.Fernandez-Catalan, H.Sorimachi, K.Suzuki, and W.Bode (2001).
Structural basis for possible calcium-induced activation mechanisms of calpains.
  Biol Chem, 382, 753-766.  
11717497 J.Jia, N.Borregaard, K.Lollike, and M.Cygler (2001).
Structure of Ca(2+)-loaded human grancalcin.
  Acta Crystallogr D Biol Crystallogr, 57, 1843-1849.
PDB codes: 1k94 1k95
11525164 J.Jia, S.Tarabykina, C.Hansen, M.Berchtold, and M.Cygler (2001).
Structure of apoptosis-linked protein ALG-2: insights into Ca2+-induced changes in penta-EF-hand proteins.
  Structure, 9, 267-275.
PDB code: 1hqv
11517927 K.Sato, and S.Kawashima (2001).
Calpain function in the modulation of signal transduction molecules.
  Biol Chem, 382, 743-751.  
11238954 M.Azam, S.S.Andrabi, K.E.Sahr, L.Kamath, A.Kuliopulos, and A.H.Chishti (2001).
Disruption of the mouse mu-calpain gene reveals an essential role in platelet function.
  Mol Cell Biol, 21, 2213-2220.  
11725957 N.Takeuchi, H.Ito, K.Namiki, and A.Kamei (2001).
Effect of calpain on hereditary cataractous rat, ICR/f.
  Biol Pharm Bull, 24, 1246-1251.  
11517929 P.Cottin, V.F.Thompson, S.K.Sathe, A.Szpacenko, and D.E.Goll (2001).
Autolysis of mu- and m-calpain from bovine skeletal muscle.
  Biol Chem, 382, 767-776.  
11342050 T.Moldoveanu, C.M.Hosfield, Z.Jia, J.S.Elce, and P.L.Davies (2001).
Ca(2+)-induced structural changes in rat m-calpain revealed by partial proteolysis.
  Biochim Biophys Acta, 1545, 245-254.  
11714909 X.Xie, M.D.Dwyer, L.Swenson, M.H.Parker, and M.C.Botfield (2001).
Crystal structure of calcium-free human sorcin: a member of the penta-EF-hand protein family.
  Protein Sci, 10, 2419-2425.
PDB code: 1juo
11516996 Y.Huang, and K.K.Wang (2001).
The calpain family and human disease.
  Trends Mol Med, 7, 355-362.  
11371436 Z.Jia, V.Petrounevitch, A.Wong, T.Moldoveanu, P.L.Davies, J.S.Elce, and J.S.Beckmann (2001).
Mutations in calpain 3 associated with limb girdle muscular dystrophy: analysis by molecular modeling and by mutation in m-calpain.
  Biophys J, 80, 2590-2596.  
11114499 A.Lewit-Bentley, and S.Réty (2000).
EF-hand calcium-binding proteins.
  Curr Opin Struct Biol, 10, 637-643.  
10825211 J.S.Arthur, J.S.Elce, C.Hegadorn, K.Williams, and P.A.Greer (2000).
Disruption of the murine calpain small subunit gene, Capn4: calpain is essential for embryonic development but not for cell growth and division.
  Mol Cell Biol, 20, 4474-4481.  
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.