FASEB SRC “Biology of Calpains in Health and Disease” Co-Organizers: James Geddes and Peter Greer July 21-26, 2013, Saxtons River, Vermont, USA Introduction: 12:00~12:15, July 23 (Tue), 2013 Discussion: 11:30~12:15, July 24 (Wed), 2013 Revised: September 20 (Fri), 2013 Calpain nomenclature Ref: http://www.calpain.net/ Hiro Sorimachi, IGAKUKEN Peter Davies, Queen’s University A brief history of structures of the conventional calpains Present situation: • Two different numbering exist. • “domain I” is too small to be called domain. Proposed domain structure, color, and nomenclature CysPc: calpain-like cysteine protease core motif [cd00044] defined in the conserved domain database (CDD) of National Center for Biotechnology Information (NCBI). Calpain domain nomenclature MIT: microtubule interaction and transport TML: long transmembrane motif SOL SOL: small optic lobes TPR Zf: zinc-finger motif TPR: tetratricopeptide repeats UBA: ubiquitin associated domain PUB: Peptide:N-glycanase/UBA or UBX-containing Calpain subunit name = Gene product name Human gene Chr. location Gene product Aliases Classical? Ubiquitous? Catalytic subunits μ-calpain large subunit (μCL), CAPN1 11q13 CAPN1 ✔ ✔ μCANP/calpain-I large subunit, μ80K m-calpain large subunit (mCL), CAPN2 1q41-q42 CAPN2 ✔ ✔ mCANP/calpain-II large subunit, m80K CAPN3 15q15.1-q21.1 CAPN3 p94, calpain-3, calpain-3a, nCL-1 ✔ CAPN5 11q14 CAPN5 hTRA-3, nCL-3 ✔ CAPN6 Xq23 CAPN6 calpamodulin, CANPX CAPN7 3p24 CAPN7 PalBH ✔ CAPN8 1q41 CAPN8 nCL-2, calpain-8, calpain-8a ✔ CAPN9 1q42.11-q42.3 CAPN9 nCL-4, calpain-9, calpain-9a ✔ CAPN10 2q37.3 CAPN10 calpain-10a (exon 8 is skipped) ✔ CAPN11 6p12 CAPN11 ✔ CAPN12 19q13.2 CAPN12 calpain-12a, calpain-12A ✔ CAPN13 2p22-p21 CAPN13 ✔ ✔ CAPN14 2p23.1-p21 CAPN14 ✔ ✔ CAPN15/SOLH 16p13.3 CAPN15 SOLH ✔ CAPN16/C6orf103 6q24.3 CAPN16 Demi-calpain, C6orf103 ✔ Regulatory subunits CAPNS1 19q13.1 CAPNS1 CANP/calpain small subunit, 30K, css1, CAPN4 n.a. ✔ CAPNS2 16q12.2 CAPNS2 calpain small subunit 2, 30K-2, css2 n.a. ✔ Calpain inhibitor CAST 5q15 CAST calpastatin, CANP inhibitor n.a. ✔ Remaining issue: how about alternatively spliced products? Nomenclature of human calpain enzymes ~ name ”calpain” is for an enzyme ~ Enzyme name Native subunit composition in vitro subunit composition Aliases calpain-1 CAPN1+CAPNS1 [CAPN1/S1] ← μ-calpain, μCANP, calpain-I calpain-2 CAPN2+CAPNS1 [CAPN2/S1] ← m-calpain, mCANP, calpain-II CAPN3+TTN (myofibril) (CAPN3) (n=1, 2) [CAPN3/3] calpain-3 n n-calpain, calpain-3 CAPN3+? (cytosol) CAPN3+PLEIAD calpain-5 CAPN5+? calpain-6 CAPN6+? calpain-7 CAPN7+? calpain-8 - (CAPN8)n (n=1, 2, 3, …) G-calpain calpain-8/9 CAPN8+CAPN9 [CAPN8/9] calpain-9 - CAPN9+CAPNS1 [CAPN9/S1] calpain-10 CAPN10+? CAPN10 (CAPN11) ? calpain-11 2 μ/m-calpain (Chicken) CAPN11+CAPNS1 (Chicken) calpain-12 CAPN12+? calpain-13 CAPN13+? calpain-14 CAPN14+? calpain-15 CAPN15+? calpain-16 CAPN16+? calpastatin CAST CANP inhibitor Remaining issue: how to distinguish different enzymes containing the same catalytic subunit (calpain-3, 8, 11)? OtherStructure species and function (1) – fly of humanand nematode calpains Gene Calpain CalpA, CalpB D. melanogaster CalpC CalpD/Sol CeC06G4.2 CeT04A8.16 CeY47H10A.1 CeY39A3CL.5 tra-3/CeLLC1.1 CeY77E11A.10 CeY77E11A.11 C. elegans F44F1.3 T11A5.6 W05G11.4 W04A4.4 F47F6.9 H25P06.45 Joyce PI et al. (2012) Y53H1B.6 PLoS Genet 8:e1002602 StructureOther speciesand function (2) - of kinetoplastids human calpains 18 calpain homologues of Trypanosoma brucei Name GeneDB ID Chromosome N-terminus Catalytic triad Length (aa) Domains Group TbCALP1.1 Tb927.1.2100 1 MSEFELMS SHN 1146 I,II,III,C 1 TbCALP1.2 Tb927.1.2110 1 MSSRNGSL SHN 682 I,II,III,C 1 TbCALP1.3 Tb927.1.2120 1 MGCGASST YHN 732 I,II,III,C 1 TbSKCRP1.4 Tb927.1.2150 1 MGLFLSKQ – – – 130 I 3 TbSKCRP1.5 Tb927.1.2160 1 MGCIQSTV – – – 140 I 3 TbSKCRP1.6 Tb927.1.2230 1 MGCGGSKT – – – 123 I 3 TbSKCRP1.7 Tb927.1.2260 1 MGCGGSTT – – – 130 I 3 TbCALP4.1CAP5.5 Tb04.1D20.740 4 MGCGGSKV SYN 853 I,II,III,C 1 TbCALP4.2 Tb04.1D20.770 4 MTSSGGLL SSN 784 I,II,III,C 1 TbCALP6.1 Tb06.2N9.670 6 MVVSLSGY SHS 1010 I,II,III,C 2 TbSKCRP7.1 Tb07.5F10.560 7 MSDITYEN – – – 115 I 3 TbCALP9.1 Tb09.160.5550 9 MMQASADG CYN 856 I,II,III,C 1 TbCALP10.1 Tb10.389.0470 10 MQVPTDQL KT– 678 I,II,III,C 2 TbCALP10.2 Tb10.70.5950 10 MATTLDDL –HH 1594 I,II,III,C 2 TbSKCRP10.3 Tb10.70.5060 10 MTELVPEA – – – 484 I 3 TbCALP11.1 Tb11.47.0035 11 MNYQAITE CQN/CQN/CQN 6145 3xII,2xIII 4 TbCALP11.2 Tb11.47.0036 11 MNEHSHEL YCC 1389 I,II,III,C 5 TbCALP11.3 Tb11.02.2240 11 MRHIQRIS CHN 1053 I,II,III,C 2 cf. Leishmania major: 27 genes Trypanosoma cruzi: 24 genes Ersfeld K et al. (2005) J Mol Evol 61:742–757 StructureOther and speciesfunction (3)of human - Plants calpains gene: defective kernel 1 (dek1) enzyme: DEK1, phytocalpain domains: TML-CysPc-C2L Lid SE et al. (2002) Proc Natl Acad Sci USA 99:5460-5465 Liang Z et al. (2013) Plant J doi:10.1111/tpj.12235 StructureOther species and function (4) – ofFungi human and calpainsyeasts Sorimachi H et al. (2011) Proc Jpn Acad Ser B Phys Biol Sci 87:287-327 .