2H5I

Crystal structure of caspase-3 with inhibitor Ac-DEVD-Cho

Summary for 2H5I

• Entry DOI: 10.2210/pdb2h5i/pdb
• Related: 2H5J 2H65
• Related PRD ID: PRD_000422
• Descriptor: caspase-3, p17 subunit, caspase-3, p12 subunit, Ac-DEV(ASJ), ... (4 entities in total)
• Functional Keywords: enzyme catalysis, cysteine protease, apoptosis, induced fit, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human); More
• Cellular location: Cytoplasm: P42574 P42574
• Total number of polymer chains: 3
• Total formula weight: 28271.26

Authors

Fang, B.,Boross, P.I.,Tozser, J.,Weber, I.T. (deposition date: 2006-05-26, release date: 2006-09-19, Last modification date: 2023-11-15)

Primary citation

Fang, B.,Boross, P.I.,Tozser, J.,Weber, I.T.
Structural and kinetic analysis of caspase-3 reveals role for s5 binding site in substrate recognition
J.Mol.Biol., 360:654-666, 2006

PubMed Abstract: The molecular basis for the substrate specificity of human caspase-3 has been investigated using peptide analog inhibitors and substrates that vary at the P2, P3, and P5 positions. Crystal structures were determined of caspase-3 complexes with the substrate analogs at resolutions of 1.7 A to 2.3 A. Differences in the interactions of caspase-3 with the analogs are consistent with the Ki values of 1.3 nM, 6.5 nM, and 12.4 nM for Ac-DEVD-Cho, Ac-VDVAD-Cho and Ac-DMQD-Cho, respectively, and relative kcat/Km values of 100%, 37% and 17% for the corresponding peptide substrates. The bound peptide analogs show very similar interactions for the main-chain atoms and the conserved P1 Asp and P4 Asp, while interactions vary for P2 and P3. P2 lies in a hydrophobic S2 groove, consistent with the weaker inhibition of Ac-DMQD-Cho with polar P2 Gln. S3 is a surface hydrophilic site with favorable polar interactions with P3 Glu in Ac-DEVD-Cho. Ac-DMQD-Cho and Ac-VDVAD-Cho have hydrophobic P3 residues that are not optimal in the polar S3 site, consistent with their weaker inhibition. A hydrophobic S5 site was identified for caspase-3, where the side-chains of Phe250 and Phe252 interact with P5 Val of Ac-VDVAD-Cho, and enclose the substrate-binding site by conformational change. The kinetic importance of hydrophobic P5 residues was confirmed by more efficient hydrolysis of caspase-3 substrates Ac-VDVAD-pNA and Ac-LDVAD-pNA compared with Ac-DVAD-pNA. In contrast, caspase-7 showed less efficient hydrolysis of the substrates with P5 Val or Leu compared with Ac-DVAD-pNA. Caspase-3 and caspase-2 share similar hydrophobic S5 sites, while caspases 1, 7, 8 and 9 do not have structurally equivalent hydrophobic residues; these caspases are likely to differ in their selectivity for the P5 position of substrates. The distinct selectivity for P5 will help define the particular substrates and signaling pathways associated with each caspase.

PubMed: 16781734
DOI: 10.1016/j.jmb.2006.05.041

Experimental method

X-RAY DIFFRACTION (1.69 Å)