PDBsum entry 2dko

Hydrolase/hydrolase inhibitor

PDB id: 2dko

Contents

Protein chains

146 a.a. *

103 a.a. *

Ligands

ASP-GLU-VAL-ASP-0QE

Waters ×335

* Residue conservation analysis

PDB id:

2dko

Name:

Hydrolase/hydrolase inhibitor

Title:

Extended substrate recognition in caspase-3 revealed by high resolution x-ray structure analysis

Structure:

Caspase-3. Chain: a. Fragment: caspase-3 p17 subunit, residues 29-174. Engineered: yes. Caspase-3. Chain: b. Fragment: caspase-3 p12 subunit, residues 175-277. Engineered: yes. Mutation: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: chemically synthesized

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.06Å R-factor: 0.142 R-free: 0.175

Authors:

P.R.E.Mittl,R.Ganesan,S.Jelakovic,M.G.Grutter

Key ref:

R.Ganesan et al. (2006). Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis. J Mol Biol, 359, 1378-1388. PubMed id: 16787777 DOI: 10.1016/j.jmb.2006.04.051

Date:

12-Apr-06 Release date: 04-Jul-06

Protein chain

P42574  (CASP3_HUMAN) -  Caspase-3 from Homo sapiens

Seq: 277 a.a.

Struc: 146 a.a.

Protein chain

P42574  (CASP3_HUMAN) -  Caspase-3 from Homo sapiens

Seq: 277 a.a.

Struc: 103 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.4.22.56 - caspase-3.

DOI no: 10.1016/j.jmb.2006.04.051

J Mol Biol 359:1378-1388 (2006)

PubMed id: 16787777

Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis.

R.Ganesan, P.R.Mittl, S.Jelakovic, M.G.Grütter.

ABSTRACT

Caspases are cysteine proteases involved in the signalling cascades of programmed cell death in which caspase-3 plays a central role, since it propagates death signals from intrinsic and extrinsic stimuli to downstream targets. The atomic resolution (1.06 Angstroms) crystal structure of the caspase-3 DEVD-cmk complex reveals the structural basis for substrate selectivity in the S4 pocket. A low-barrier hydrogen bond is observed between the side-chains of the P4 inhibitor aspartic acid and Asp179 of the N-terminal tail of the symmetry related p12 subunit. Site-directed mutagenesis of Asp179 confirmed the significance of this residue in substrate recognition. In the 1.06 Angstroms crystal structure, a radiation damage induced rearrangement of the inhibitor methylketone moiety was observed. The carbon atom that in a substrate would represent the scissile peptide bond carbonyl carbon clearly shows a tetrahedral coordination and resembles the postulated tetrahedral intermediate of the acylation reaction.

Selected figure(s)

Figure 3.
Figure 3. Superposition of active sites in the 1.06 Å and 1.7 Å resolution structures with carbon atoms shown in cyan and magenta, respectively. The F[obs](1.06 Å) -(F[obs](1.7 Å)) (f[calc]^(1.06 Å)) map was contoured at +5s (green) and -5s (red) levels. The 2F[obs](1.06 Å) -(F[calc]^(1.06 Å)) (f[calc]^(1.06 Å)) map contoured at +3s is shown in grey.

Figure 6.
Figure 6. Active site geometry of the (a) 1.7 Å and (b) 1.06 Å resolution structures. Putative hydrogen bonds and general distances are shown in red and grey, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 1378-1388) copyright 2006.

Figures were selected by an automated process.