Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth L]SCOP2 FamilyPenta-EF-hand proteins 8025811 4003019 SCOP2 (2022-06-29)
A [auth L]SCOP2 FamilyCalpain large subunit, middle domain (domain III) 8025816 4002433 SCOP2 (2022-06-29)
A [auth L]SCOP2 FamilyCalpain large subunit, catalytic domain (domain II) 8025818 4000875 SCOP2 (2022-06-29)
A [auth L]SCOP2 SuperfamilyEF-hand 8038190 3001983 SCOP2 (2022-06-29)
A [auth L]SCOP2 SuperfamilyCalpain large subunit, middle domain (domain III) 8038195 3001233 SCOP2 (2022-06-29)
A [auth L]SCOP2 SuperfamilyCysteine proteinases 8038197 3001808 SCOP2 (2022-06-29)
B [auth S]SCOP2 FamilyPenta-EF-hand proteins 8025820 4003019 SCOP2 (2022-06-29)
B [auth S]SCOP2 SuperfamilyEF-hand 8038199 3001983 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth L]Calpain_IIIe1kfuL7 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Galactose-binding domain-likeF: Calpain_IIIECOD (1.6)
A [auth L]EF-hand_8e1kfuL6 A: alpha arraysX: EF-handH: EF-hand-relatedT: EF-handF: EF-hand_8ECOD (1.6)
A [auth L]EF-hand_7_2e1kfuL2 A: alpha arraysX: EF-handH: EF-hand-relatedT: EF-handF: EF-hand_7_2ECOD (1.6)
A [auth L]Peptidase_C2e1kfuL5 A: a+b complex topologyX: Cysteine proteinases-likeH: Cysteine proteinases (From Topology)T: Cysteine proteinasesF: Peptidase_C2ECOD (1.6)
B [auth S]EF-hand_7e1kfuS1 A: alpha arraysX: EF-handH: EF-hand-relatedT: EF-handF: EF-hand_7ECOD (1.6)
B [auth S]EF-hand_8e1kfuS2 A: alpha arraysX: EF-handH: EF-hand-relatedT: EF-handF: EF-hand_8ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A [auth L]3.90.70.10 Alpha Beta Alpha-Beta Complex Cathepsin B Chain ACATH (4.3.0)
A [auth L]2.60.120.380 Mainly Beta Sandwich Jelly Rolls CATH (4.3.0)
A [auth L]1.10.238.10 Mainly Alpha Orthogonal Bundle Recoverin domain 1CATH (4.3.0)
B [auth S]1.10.238.10 Mainly Alpha Orthogonal Bundle Recoverin domain 1CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth L]PF13833EF-hand domain pair (EF-hand_8)EF-hand domain pair- Domain
A [auth L]PF00648Calpain family cysteine protease (Peptidase_C2)Calpain family cysteine protease- Family
A [auth L]PF01067Calpain large subunit, domain III (Calpain_III)Calpain large subunit, domain IIIThe function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth L]M-CALPAIN LARGE SUBUNIT
B [auth S]M-CALPAIN SMALL SUBUNIT

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
calpain-2  M-CSA #589

Calpain is an intracellular, cytostolic, calcium dependent cysteine protease containing a conserved papain-like catalytic fold. Thus, in the presence of clacium, calpain catalyses the hydrolysis of peptide bonds in proteins. Two major, heterodimeric isoforms exist, micro- and m-calpain, which differ in their concentration requirements of calcium ions for activation. Calpains are the only known mammalian enzymes that combine protease activity with dependence on calcium ion binding to EF-hands in one molecule.

Calcium regulates calpain-1 activity by affecting the orientation of the two catalytic lobes (domains I and II). calcium binding occurs at multiple sites, including EF-hands and loops near the active site itself. At low calcium levels, domains I and II are locked by the regulatory domains of the proteins in an open, inhibited conformation, where the catalytic residues are too far apart to form the triad. (Cys of domain I, His and Asp of domain II).

Calpain exists in animals, but not in plants, yeast or bacteria. Through proteolysis of key cellular components, calpain plays a significant physiological role and is involved in a variety of cellular functions, including nerve growth, muscle homeostasis, signal transduction and apoptosis. Calpains have been known as biomodulators since their physiological activity involves cleavage of substrates at inter-domain boundaries, hence modulating the function of these substrates rather than digesting them.

Excessive activation and calcium dependent proteolysis by calpain has been implicated in neurodegenerative and demyelinating diseases including cerebral ischemia, ischemic myocardial infarction, spinal cord injury, muscular dystrophy and cataract. Calpain inhibition should help to control symptoms, hence calpains are ideal targets for pharmacological intervention.

The catalytic triad is not assembled prior to calcium binding. The calcium ion induces conformational changes to bring together the domain I Cis residue and the domain II His and Asp residues. In the inactive form, the residues are too far apart to form the triad since the Cis-His ion pair cannot be formed over such a distance. Calpain is also capable of autoproteolysis.

Defined by 5 residues: GLN:A-98 [auth L-99]CYS:A-104 [auth L-105]HIS:A-261 [auth L-262]ASN:A-285 [auth L-286]TRP:A-287 [auth L-288]
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