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protease (CysPc) domain structure
CAPN1, human:
CAPN1, rat:
  • 1KXR C115S, residues 27-356; plus 2Ca2+
  • 1TL9  C115S, residues 27-356; plus 2Ca2+, leupeptin
  • 1TLO  C115S, residues 27-356; plus 2Ca2+, E-64
  • 2G8E  residues 27-356; plus 2Ca2+, SNJ-1715
  • 2G8J  residues 27-356; plus 2Ca2+, SNJ-1945
  • 2NQG  residues 27-356; plus 2Ca2+, WR18(S,S)
  • 2NQI  residues 27-356; plus 2Ca2+, WR13(R,R)
  • 2R9C  residues 27-356; plus 2Ca2+, ZLAK-3001
  • 2R9F residues 27-356; plus 2Ca2+, ZLAK-3002
CAPN2, rat:
  • 1MDW  C105S, residues 17-346; plus 2Ca2+
CAPN8, human:
  • 2NQA  residues 23-346; plus 1.5Ca2+*, leupeptin
    (*dimer structure contains 3 Ca2+ ions.)
CAPN9, human:


Fig. 10 Comparison of the 3D structures of the CysPc domains of mammalian calpains.

The CysPc domains of active Ca2+-bound CAPN1[μCL] (PDB accession No: 2ARY, blue) (Davis et al., 2007), CAPN2[mCL] (1MDW, red) (Moldoveanu et al., 2003), CAPN8[nCL-2] (2NQA, white), and CAPN9[nCL-4] (1ZIV, green) (Davis et al., 2007), and inactive non-Ca2+-bound CAPN2[mCL] (1KFU, black) (Strobl et al., 2000) were aligned at their PC1 (protease core domain 1) domains using MolFeat Ver.4.6 (FiatLux Inc.), and represented as a cross-eye stereo ribbon scheme. Cys, Trp, His, and Asn indicate C115/105/105/97 (for CAPN1[μCL], CAPN2[mCL], CAPN8[nCL-2], and CAPN9[nCL-4], respectively), W116/106/106/98, H272/262/262/254, and N296/286/286/278, respectively, which are active site triad residues and the Trp residue “interfering” with them in CAPN2[mCL] and CAPN8[nCL-2]. Whereas active CAPN1[μCL], CAPN2[mCL], and CAPN8[nCL-2] were almost completely aligned, inactive CAPN2[mCL] was only moderately aligned, and active CAPN9[nCL-4] was misaligned (see also Table 7).

Abbreviations used for domain names:
CysPc: calpain-like cysteine protease sequence motif defined in the conserved domain database at the National Center for Biotechnology Information (cd00044), which is composed of two protease core domains 1 and 2 (PC1 and PC2).
PC1: protease core domain 1
PC2: protease core domain 2
CBS-1: Ca2+-binding site 1 in PC1 domain
CBS-2: Ca2+-binding site 2 in PC2 domain

Table 7 Similarities of the 3D structures of mammalian calpain protease domains

Pairwise alignment of each pair of the CysPc domains of the calpains indicated was performed using Dali server (Holm and Sander, 1993). The upper right (in blue) values indicate the Z-scores (the number of standard deviations; the larger the Z value, the more similar the domains; Z=2, 5, and 8 correspond to P=0.023, 2.9x10-7, and <10-15, respectively; all the Z-scores are >8, indicating P<10-15). The lower left (in red) values show the RMSD (root-mean-square deviation, Å). Three values in each column, x (y / z), correspond to when CysPc (x), PC1 (protease core domain 1) (y), or PC2 (z) domains are compared with each other, respectively). All the structures except for 1KFU are Ca2+-bound active structures. Note that all the active structures except CAPN9 are aligned with an RMSD not more than 1.2 Å, and that PC1 and PC2 of CAPN9 are also well aligned (RMSD≤1.7 Å) although the whole CysPc of CAPN9 is not (RMSD>6 Å) (see also Fig. 10). Species: 1MDW, rat; all others, human.

CAPN1/Ca (2ARY) [Z-scores----->] 47.2 (31.5/24.8) 46.8 (32.1/25.1) 29.3 (25.6/23.8) 27.8 (25.0/16.4)
CAPN2/Ca (1MDW) 1.0 (1.2/0.7)   46.6 (32.3/25.1) 30.8 (27.3/24.3) 30.8 (25.4/16.5)
CAPN8/Ca (2NQA) 1.0 (1.0/0.6) 1.1 (1.1/0.7) values are for
[CysPc (PC1/PC2)]
29.8 (26.8/23.5) 28.1 (25.5/16.3)
CAPN9/Ca (1ZIV) 6.6 (1.7/1.1) 6.6 (1.2/0.9) 6.2 (1.5/1.0)   25.1 (24.2/15.9)
CAPN2 (1KFU) 3.7 (2.1/2.4) 3.8 (1.6/2.3) 3.9 (1.9/2.4) -* (1.6/2.5) [<-----RMSD]
*: Dali failed to compare the whole CysPc domains of 1KFU and 1ZIV because the structures were too divergent.

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