PDBsum entry: 1jxq

Hydrolase/hydrolase inhibitor

PDB id: 1jxq

Contents

Protein chains

242 a.a. *

226 a.a. *

Ligands

PHQ-GLU-VAL-ASP-CF0 ×2

Waters ×264

* Residue conservation analysis

PDB id:

1jxq

Name:

Hydrolase/hydrolase inhibitor

Title:

Structure of cleaved, card domain deleted caspase-9

Structure:

Caspase-9. Chain: a, b, c, d. Synonym: ice-lap6. Engineered: yes. Benzoxycarbonyl-val-ala-asp-fluoromethyl ketone i chain: e, f. Engineered: yes

Source:

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

Biol. unit:

Hexamer (from PQS)

Resolution:

2.80Å R-factor: 0.233 R-free: 0.275

Authors:

M.Renatus,H.R.Stennicke,F.L.Scott,R.C.Liddington,G.S.Salvese

Key ref:

M.Renatus et al. (2001). Dimer formation drives the activation of the cell death protease caspase 9. Proc Natl Acad Sci U S A, 98, 14250-14255. PubMed id: 11734640 DOI: 10.1073/pnas.231465798

Date:

08-Sep-01 Release date: 12-Dec-01

Protein chains

P55211  (CASP9_HUMAN) -  Caspase-9

Seq: 416 a.a.

Struc: 242 a.a.*

Protein chains

P55211  (CASP9_HUMAN) -  Caspase-9

Seq: 416 a.a.

Struc: 226 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.3.4.22.62 - Caspase-9.

 Gene Ontology (GO) functional annotation 

• Biological process: apoptosis (2 terms)
• Biochemical function: cysteine-type peptidase activity (2 terms)

DOI no: 10.1073/pnas.231465798

Proc Natl Acad Sci U S A 98:14250-14255 (2001)

PubMed id: 11734640

Dimer formation drives the activation of the cell death protease caspase 9.

M.Renatus, H.R.Stennicke, F.L.Scott, R.C.Liddington, G.S.Salvesen.

ABSTRACT

A critical step in the induction of apoptosis is the activation of the apoptotic initiator caspase 9. We show that at its normal physiological concentration, caspase 9 is primarily an inactive monomer (zymogen), and that activity is associated with a dimeric species. At the high concentrations used for crystal formation, caspase 9 is dimeric, and the structure reveals two very different active-site conformations within each dimer. One site closely resembles the catalytically competent sites of other caspases, whereas in the second, expulsion of the "activation loop" disrupts the catalytic machinery. We propose that the inactive domain resembles monomeric caspase 9. Activation is induced by dimerization, with interactions at the dimer interface promoting reorientation of the activation loop. These observations support a model in which recruitment by Apaf-1 creates high local concentrations of caspase 9 to provide a pathway for dimer-induced activation.

Selected figure(s)

Figure 3.
Fig. 3. The dimer interface. This view focuses on interactions that influence dimer formation. (A) Stereoview as in Fig. 2A showing the side chains of Phe-390 and Tyr-331 and the catalytic Cys-285 in the active (Left) and inactive (Right) catalytic domains, within the dimeric structure. (B) Stereoview of a superposition of the inactive monomer (gray) onto the active one (red). Rotation of Phe-390 about C^ -C^ occurs in the transition from the inactive to the active conformation, allowing a compensatory rotation of Tyr-331 around its C^ -C^ . This in turn may help to promote the catalytic conformation of Cys-285. The yellow side-chain represents the position of Phe-390' in a hypothetical dimer made from two active catalytic domains. Note that it would clash with the active conformation of Phe-390, eliminating the possibility of having two active monomers in this dimer.

Figure 4.
Fig. 4. The mechanism of zymogen activation. Caspase 9 exists as a monomer at physiologic concentrations, with an exposed activation loop that renders the enzyme latent. (A) During dimerization, the activation loop (red) of the left domain is drawn into a pocket on the right domain. (B) The hydrophobic pocket, bordered by Pro-324, Phe-240f, and Phe-393 in the right domain, accepts Phe-334 and Phe-337 from the left domain. This locks into place the priming bulge (Ser-330-Ser-339) of the activation loop, enabling Trp-340 and Arg-341 to sink into their substrate-binding conformation, and simultaneously allowing hydrogen bonding to the segment following Cys-285. This transition generates catalytic potential in the left domain.

Figures were selected by an automated process.