Caspase-3/Sandbox
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| Crystal Structure of Unliganded Human Caspase-3 | |||||||||
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| Gene: | CASP3 OR CPP32 (Homo sapiens) | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Structure & FunctionStructure & Function
StructureStructure
(Structural Description) Caspase-3 chains are classified as alpha/beta, with one chain containing a 3-layer(aba) sandwich with Rossmann fold topology (This fold is made up of three or more parallel beta strands linked by two alpha helices in the topological order beta-alpha-beta-alpha-beta) and another chain containing a 2-layer sandwich with alpha-beta plaits.
The active form is made up of two chains, of which can be kept in its inactive form by inhibitors such as DEVD-CHO seen in 1pau.
DomainsDomains
Heterotetramer that consists of two anti-parallel arranged heterodimers, each one formed by a 17 kDa (p17) and a 12 kDa (p12) subunit (http://www.uniprot.org/uniprot/P42574)
Folds and MotifsFolds and Motifs
Posttranslational ModificationsPosttranslational Modifications
Caspase-3 is translated as a zymogen. Activation occurs via cleavage by initiator caspases, such as caspase-8, -9, and -10, and by granzyme B to generate the p12(small) and p17(large) subunits. (http://www.uniprot.org/uniprot/P42574)
S-NitrosylationS-Nitrosylation
An ambient level of nitric oxide has antiapoptotic effects via S-nitrosylation of caspase-3 zymogens at its catalytic Cys163 residue perhaps because it directly associates with all 3 NOS isoforms. S-nitrosylation effectively inhibits the enzyme activity of caspase-3 (Mannick, 2007). NO and S-nitrosoglutathione (GSNO) reacts nonspecifically to all cysteine residues of caspase-3 (Mitchell, 2005). Caspase-3 nitrosylation at a second cysteine residue (Cys47, Cys220, or Cys 264) may have further antiapoptotic effects by leading to its association with acid sphingomyelinase (ASM). ASM inhibits cleavage and activation of caspase-3 by initiator caspases, such as caspase-8 and caspase-9 (Mannick, 2007).
Thioredoxin, the main intracellular oxidoreductase, does not inhibit caspase-3 activity. However, Trx-Cys73-SNO inhibits apoptosis by decreasing caspase-3 activity via transnitrosylation at Cys163 catalytic residue. This reaction is reversible, although this is not as likely since Cys163 on caspase-3 is more nucleophilic than Cys73 on Trx. GSNO is capable of transferring its nitroso-group to Trx-Cys73, which in turn can S-nitrosylate caspase-3, leading to inactive caspase-3 (Mitchell, 2005).
In human B- and T-cell lines, nitrosylation of caspase-3 depends on localization: mitochondrial but not cytoplasmic caspase-3 zymogens are S-nitrosylated. S-nitrosylation may prevent improper autoactivation in the mitochondria due to close proximity in the intermembrane space (Mannick, 2001). Mitochondrial caspase-3 is released into the cytoplasm and becomes denitrosylated when FasL binds Fas receptor (Mannick, 2001). Fas receptor activation by FasL activates the extrinsic pathway of apoptosis through activation of caspase-8, which can either directly cleave procaspase-3 to caspase-3 or lead to Bid cleavage to tBid. tBID then permeates into the mitochondria, leading to cytochrome c release, apoptosome formation with caspase-9, and finally caspase-3 cleavage to its activated form. Smac/DIABLO is also released from the mitochondria and leads to inhibition of XIAP (X-linked inhibitor of apoptosis), abrogating its inhibitory effect on caspase-3 activity within the cytosol. XIAP also functions as an E3 ubiquitin ligase, targeting caspase-3 for proteasomal degradation (Nakamura, 2010). Aside from this, Fas-induced apoptosis also leads to denitrosylation of caspase-3 and therefore activation by freeing its catalytic Cys residue (Mannick, 1999). Perhaps, this denitrosylation occurs via transnitrosylation of XIAP RING domain at Cys450, which in effect inhibits its E3 ligase activity. This further prolongs caspase-3 activity by blocking its degradation, and thus promotes increased cell death (Nakamura, 2010). Thus, S-nitrosylation of caspases inhibits caspase activation and apoptosis, whereas denitrosylation activates caspases and promotes apoptosis (Mannick, 2007).
OtherOther
The first residue of caspase-3, Met1, is posttranslationally modified as N-acetylmethionine. Ser26 is possibly modified as Phosphoserine.(http://www.uniprot.org/uniprot/P42574)
Active Site/Ligand Binding/Catalytic ActivityActive Site/Ligand Binding/Catalytic Activity
This is a morph of caspase-3 from its uninhibited form to inhibition by novel irreversible inhibitor B92 ((3S)-3-({[(5S,10aS)-2-{(2S)-4-carboxy-2-[(phenylacetyl)amino]butyl}-1,3-dioxo-2,3,5,7,8,9,10,10a-octahydro-1H-[1,2,4]triazolo[1,2-a]cinnolin-5-yl]carbonyl}amino)-4-oxopentanoic acid). The involves, and . (Wang, Watt et al. 2010) When cleaved into its active form, caspase-3 is then able to bind to its substrates via recognition of DEVD consensus sequence. Caspase-3, using its active site cysteine residue, is then able to cleave the substrate at the Asp residue occupying the P4 portion of the active site. This is a (1qx3 to 2cjx)showing the binding of modified DEVD substrate (zDEVD-cmk) to the active site of caspase-3. 
Strict requirement for an Asp residue at positions P1 and P4. It has a preferred cleavage sequence of Asp-Xaa-Xaa-Asp-|- with a hydrophobic amino-acid residue at P2 and a hydrophilic amino-acid residue at P3, although Val or Ala are also accepted at this position. (http://www.uniprot.org/uniprot/P42574)
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FunctionFunction
Casp3 Involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop- helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9. Involved in the cleavage of huntingtin. Belongs to the peptidase C14A family. Heterotetramer that consists of two anti-parallel arranged heterodimers, each one formed by a 17 kDa (p17) and a 12 kDa (p12) subunit. Protein type: EC 3.4.22.56; EC 3.4.22.-; Protease; Apoptosis (http://www.phosphosite.org/proteinAction.do?id=4672&showAllSites=true)
Involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop-helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9. Involved in the cleavage of huntingtin. (Nature. 1995 Jul 6;376(6535):37-43. Identification and inhibition of the ICE/CED-3 protease necessary for mammalian apoptosis. Nicholson DW, Ali A, Thornberry NA, Vaillancourt JP, Ding CK, Gallant M, Gareau Y, Griffin PR, Labelle M, Lazebnik YA, et al.)(http://www.uniprot.org/uniprot/P42574)
(Structural insights into its function)
Caspases are proteases that function via a cysteine residue in the active site to cleave substrates after aspartic acid residues. Caspases are crucial for the initiation (e.g. caspase-8, -9, -10) and execution (e.g. caspase-3, -6, -7) of apoptosis, or programmed cell death either via the intrinsic or extrinsic pathway (Degterev, Boyce et al. 2003).
In the intrinsic pathway, stimuli such as trophic factor withdrawal, UV irradiation, chemotherapeutics, DNA damage, endoplasmic reticulum (ER) stress, activates B cell lymphoma 2 (BCL-2) homology 3 (BH3)-only proteins like Bim or Bad, leading to BCL-2-associated X protein (BAX) and BCL-2 antagonist or killer (BAK) activation and mitochondrial outer membrane permeabilization (MOMP). Following MOMP, cytochrome c is released and binds apoptotic protease-activating factor 1 (APAF1), inducing recruitment of the apoptosome and activation of caspase-9, an initiator caspase. Caspase-9 cleaves and activates effector caspases, caspase-3 and caspase-7, leading to apoptosis through cleavage of death substrates such as Inhibitor of Caspase-activated Deoxyribonuclease (ICAD) and Poly ADP ribose polymerase (PARP). Mitochondrial release of second mitochondria-derived activator of caspase (Smac/DIABLO) relieves the caspase inhibitory function of X-linked inhibitor of apoptosis protein (XIAP).
The extrinsic apoptotic pathway is initiated by the activation of death receptors, such as Fas by FasL. Fas-associated death domain protein (FADD) is recruited to the receptor along with caspase-8. This results in the dimerization and activation of caspase-8, which can then directly cleave and activate caspase-3 and caspase-7, leading to apoptosis. Crosstalk between the extrinsic and intrinsic pathways occurs through BH3-only protein BH3-interacting domain death agonist (BID) cleavage to truncated BID (tBID) by active caspase-8 (Li, Zhu et al. 1998). It has become appreciated more recently that caspase activity, specifically caspase-8, is also required for T cell growth (Alam, Cohen et al. 1999; Kennedy, Kataoka et al. 1999; Misra, Jelley-Gibbs et al. 2005), and that the location and level of active caspases within cells may be a key determinant of survival or death (Misra, Russell et al. 2007; Koenig, Russell et al. 2008). Murine αβ T cells bearing high levels of caspase activity manifest increased rates of both cell growth and cell death (Dohrman, Russell et al. 2005).
Caspase-3Caspase-3
In its inactive form, procaspase-3 consist of a large subunit and small subunit, interjected by an aspartic acid residue. This aspartate is the site recognized by activated initiator caspases, such as caspase-8 and caspase-9. Upon cleavage, procaspase-3 is separated into two subunits, p18/20 and p12/10 respectively, which heterodimerize to yield the active form of caspase-3. In its active form, caspase-3 is able to cleave substrates such as ICAD (inhibitor of caspase-activated deoxyribonuclease). Cleavage of ICAD leads to abrogation of its inhibitory effect on CAD, allowing CAD to migrate into the nucleus and cause double-strand breaks in DNA, thus contributing to apoptosis(Enari, Sakahira et al. 1998; Sakahira, Enari et al. 1998).
DiseaseDisease
Although the role of caspases in chronic neurodegenerative disease is controversial, their role in acute neurodegenerative disease, such as nerve crush injury and stroke, may be more evident. Inhibition of caspase activity increases survival of neurons. Studies have also shown that caspases are downregulated to allow for unchecked survival of neoplastic cancers and autoimmune diseases. In particular, caspase-8 has been found to be silenced in neuroblastoma and humans with mutations in caspase-8 and -10 develop ALPS (autoimmune lymphoproliferative syndrome). These raise the possibility that caspase-3 may play a role as well. Knocking out caspase-3 in 129x1/SvJ mice leads to hydrocephalus and subsequently perinatal lethality. Caspase-3 knockout in C57BL/6J however appear to have no brain abnormalities.
(Fuentes-Prior and Salvesen, 2004)
SNO-caspases have been suggested to promote cell injury and death in neurodegenerative disorders, such as Alzheimer’s, Parkinson’s and Huntington’s diseases, by transnitrosylating XIAP (Nakamura, 2010).
Evolutionarily Related ProteinsEvolutionarily Related Proteins
To date, eighteen caspases have been identified. Caspases can largely be grouped into three subfamilies in humans: inflammatory (caspase-1, -4, and -5), effector (caspase-3, -6, and -7), and initiator caspases (-2, -8, -9, and -10). Caspase-11 and -12 substitutes for caspase-4 and -5, respectively, in mice. (Fuentes-Prior and Salvesen, 2004)
Solved StructuresSolved Structures
(Links to available structures) 3PCX Caspase-3 E246A, K242A Double Mutant http://www.pdb.org/pdb/explore/explore.do?structureId=3PCX 3PD1 Caspase-3 K242A http://www.pdb.org/pdb/explore/explore.do?structureId=3PD1 3PD0 Caspase-3 E246A http://www.pdb.org/pdb/explore/explore.do?structureId=3PD03KJF 3KJF Caspase-3 bound to a covalent inhibitor http://www.pdb.org/pdb/explore/explore.do?structureId=3KJF
3ITN
3H0E
3GJQ, 3GJR, 3GJS, 3GJT
3EDQ
3DEH, 3DEI, 3DEJ, 3DEK
2CNK, 2CNL, 2CNN, 2CNO, 2CDR
2J30, 2J31, 2J32, 2J33
2C1E, 2C2K, 2C2M, 2C2O
2H51
2H5J
2H65
2DKO, 2CJX, 2CJY
1RE1
1RHJ, 1RHK, 1RHM, 1RHQ, 1RHR, 1RHU
1NME, 1NMQ, 1NMS
1CP3
1PAU
1I3O
1QX3
References & NotesReferences & Notes
Alam, A., L. Y. Cohen, et al. (1999). "Early activation of caspases during T lymphocyte stimulation results in selective substrate cleavage in nonapoptotic cells." J Exp Med 190(12): 1879-90.
Aouad, S. M., L. Y. Cohen, et al. (2004). "Caspase-3 is a component of Fas death-inducing signaling complex in lipid rafts and its activity is required for complete caspase-8 activation during Fas-mediated cell death." J Immunol 172(4): 2316-23.
Budd, R. C. (2001). "Activation-induced cell death." Curr Opin Immunol 13(3): 356-62.
Degterev, A., M. Boyce, et al. (2003). "A decade of caspases." Oncogene 22(53): 8543-67.
Dohrman, A., J. Q. Russell, et al. (2005). "Cellular FLIP long form augments caspase activity and death of T cells through heterodimerization with and activation of caspase-8." J Immunol 175(1): 311-8.
Enari, M., H. Sakahira, et al. (1998). "A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD." Nature 391(6662): 43-50.
Kennedy, N. J., T. Kataoka, et al. (1999). "Caspase activation is required for T cell proliferation." J Exp Med 190(12): 1891-6.
Koenig, A., J. Q. Russell, et al. (2008). "Spatial differences in active caspase-8 defines its role in T-cell activation versus cell death." Cell Death Differ 15(11): 1701-11.
Li, H., H. Zhu, et al. (1998). "Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis." Cell 94(4): 491-501.
Misra, R. S., D. M. Jelley-Gibbs, et al. (2005). "Effector CD4+ T cells generate intermediate caspase activity and cleavage of caspase-8 substrates." J Immunol 174(7): 3999-4009.
Misra, R. S., J. Q. Russell, et al. (2007). "Caspase-8 and c-FLIPL associate in lipid rafts with NF-kappaB adaptors during T cell activation." J Biol Chem 282(27): 19365-74.
Sakahira, H., M. Enari, et al. (1998). "Cleavage of CAD inhibitor in CAD activation and DNA degradation during apoptosis." Nature 391(6662): 96-9.
Vincent, M. S., K. Roessner, et al. (1996). "Apoptosis of Fashigh CD4+ synovial T cells by borrelia-reactive Fas-ligand(high) gamma delta T cells in Lyme arthritis." J Exp Med 184(6): 2109-17.
Wang Z, Watt W, et al. (2010) Kinetic and structural characterization of caspase-3 and caspase-8 inhibition by a novel class of irreversible inhibitors. Biochim Biophys Acta 1804(9):1817-31.
Wesselborg, S., O. Janssen, et al. (1993). "Induction of activation-driven death (apoptosis) in activated but not resting peripheral blood T cells." J Immunol 150(10): 4338-45.