PDBsum entry 3dei

Hydrolase, apoptosis

PDB id: 3dei

Contents

Protein chains

232 a.a. *

Ligands

RXB

Waters ×74

* Residue conservation analysis

PDB id:

3dei

Name:

Hydrolase, apoptosis

Title:

Crystal structures of caspase-3 with bound isoquinoline-1,3,4-trione derivative inhibitors

Structure:

Caspase-3. Chain: a, b, c, d. Synonym: casp-3, apopain, cysteine protease cpp32, yama protein, cpp- 32, srebp cleavage activity 1, sca-1, caspase-3 subunit p17, caspase- 3 subunit p12. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.80Å R-factor: 0.215 R-free: 0.291

Authors:

J.Wu,J.Du,J.Li,J.Ding

Key ref:

J.Q.Du et al. (2008). Isoquinoline-1,3,4-trione Derivatives Inactivate Caspase-3 by Generation of Reactive Oxygen Species. J Biol Chem, 283, 30205-30215. PubMed id: 18768468 DOI: 10.1074/jbc.M803347200

Date:

10-Jun-08 Release date: 02-Sep-08

Protein chains

P42574  (CASP3_HUMAN) -  Caspase-3 from Homo sapiens

Seq: 277 a.a.

Struc: 232 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.22.56 - caspase-3.

DOI no: 10.1074/jbc.M803347200

J Biol Chem 283:30205-30215 (2008)

PubMed id: 18768468

Isoquinoline-1,3,4-trione Derivatives Inactivate Caspase-3 by Generation of Reactive Oxygen Species.

J.Q.Du, J.Wu, H.J.Zhang, Y.H.Zhang, B.Y.Qiu, F.Wu, Y.H.Chen, J.Y.Li, F.J.Nan, J.P.Ding, J.Li.

ABSTRACT

Caspase-3 is an attractive therapeutic target for treatment of diseases involving disregulated apoptosis. We report here the mechanism of caspase-3 inactivation by isoquinoline-1,3,4-trione derivatives. Kinetic analysis indicates the compounds can irreversibly inactivate caspase-3 in a 1,4-dithiothreitol (DTT)- and oxygen-dependent manner, implying that a redox cycle might take place in the inactivation process. Reactive oxygen species detection experiments using a chemical indicator, together with electron spin resonance measurement, suggest that ROS can be generated by reaction of isoquinoline-1,3,4-trione derivatives with DTT. Oxygen-free radical scavenger catalase and superoxide dismutase eliciting the inactivation of caspase-3 by the inhibitors confirm that ROS mediates the inactivation process. Crystal structures of caspase-3 in complexes with isoquinoline-1,3,4-trione derivatives show that the catalytic cysteine is oxidized to sulfonic acid (-SO(3)H) and isoquinoline-1,3,4-trione derivatives are bound at the dimer interface of caspase-3. Further mutagenesis study shows that the binding of the inhibitors with caspase-3 appears to be nonspecific. Isoquinoline-1,3,4-trione derivative-catalyzed caspase-3 inactivation could also be observed when DTT is substituted with dihydrolipoic acid, which exists widely in cells and might play an important role in the in vivo inactivation process in which the inhibitors inactivate caspase-3 in cells and then prevent the cells from apoptosis. These results provide valuable information for further development of small molecular inhibitors against caspase-3 or other oxidation-sensitive proteins.

Selected figure(s)

Figure 6.
Crystal structures of caspase-3 in complexes with inhibitors. A, a ribbon diagram shows the overall structure of caspase-3. B, molecular surface maps represent the hydrophobic pocket with the bound inhibitors. C, a stereo view shows the composition of the hydrophobic pocket at the dimer interface and the oxidation of the catalytic cysteine (Cys^163) to sulfonic acid. D, the four inhibitors are superimposed at the binding site within bound compounds I, II, III, and IV colored in magenta, green, cyan, and yellow, respectively. E, a stereo view shows the catalytic active site of molecule C. The 2F[o] - F[c] sa_omit_map (1σ contour level) for the oxidized catalytic cysteine and the residues nearby are shown with cyan meshes.

Figure 7.
Proposed scheme for the catalytic inactivation of caspase-3 by isoquinoline-1,3,4-trione derivatives through redox cycling. In the presence of DTT in vitro and possibly dihydrolipoic acid in vivo, isoquinoline-1,3,4-trione derivatives rapidly undergo reduction to the corresponding semiquinone anion radicals (RQ^-). The reaction is reversible in the presence of atmospheric oxygen by reduction oxygen to ROS. The farther oxidation of DTT and dihydrolipoic acid intermediate also could generate ROS (38, 39). The produced ROS catalyzes the step by step oxidation of the active site cysteine of caspase-3 to the sulfonic acid. The semiquinone anion radicals may also contribute to the specific oxidation of the catalytic cysteine via a intermediate (Caspase-SH/RQ^-). Caspase-SH, caspase-SOH, caspase-SO[2]H, and caspase-SO[3]H represent the thiol, sulfenic, sulfinic, and sulfonic acid states of the catalytic cysteine.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 30205-30215) copyright 2008.

Figures were selected by an automated process.