PDBsum entry 1z6t

Apoptosis

PDB id: 1z6t

Contents

Protein chain

576 a.a. *

Ligands

ADP ×4

Waters ×803

* Residue conservation analysis

PDB id:

1z6t

Name:

Apoptosis

Title:

Structure of the apoptotic protease-activating factor 1 bound to adp

Structure:

Apoptotic protease activating factor 1. Chain: a, b, c, d. Fragment: apaf-1, residues 1-591. Synonym: apaf-1. Engineered: yes

Source:

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

Resolution:

2.21Å R-factor: 0.192 R-free: 0.244

Authors:

S.J.Riedl,W.Li,Y.Chao,R.Schwarzenbacher,Y.Shi

Key ref:

S.J.Riedl et al. (2005). Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature, 434, 926-933. PubMed id: 15829969 DOI: 10.1038/nature03465

Date:

23-Mar-05 Release date: 19-Apr-05

Protein chains

O14727  (APAF_HUMAN) -  Apoptotic protease-activating factor 1 from Homo sapiens

Seq: 1248 a.a.

Struc: 576 a.a.

DOI no: 10.1038/nature03465

Nature 434:926-933 (2005)

PubMed id: 15829969

Structure of the apoptotic protease-activating factor 1 bound to ADP.

S.J.Riedl, W.Li, Y.Chao, R.Schwarzenbacher, Y.Shi.

ABSTRACT

Apoptosis is executed by caspases, which undergo proteolytic activation in response to cell death stimuli. The apoptotic protease-activating factor 1 (Apaf-1) controls caspase activation downstream of mitochondria. During apoptosis, Apaf-1 binds to cytochrome c and in the presence of ATP/dATP forms an apoptosome, leading to the recruitment and activation of the initiator caspase, caspase-9 (ref. 2). The mechanisms underlying Apaf-1 function are largely unknown. Here we report the 2.2-A crystal structure of an ADP-bound, WD40-deleted Apaf-1, which reveals the molecular mechanism by which Apaf-1 exists in an inactive state before ATP binding. The amino-terminal caspase recruitment domain packs against a three-layered alpha/beta fold, a short helical motif and a winged-helix domain, resulting in the burial of the caspase-9-binding interface. The deeply buried ADP molecule serves as an organizing centre to strengthen interactions between these four adjoining domains, thus locking Apaf-1 in an inactive conformation. Apaf-1 binds to and hydrolyses ATP/dATP and their analogues. The binding and hydrolysis of nucleotides seem to drive conformational changes that are essential for the formation of the apoptosome and the activation of caspase-9.

Selected figure(s)

Figure 1.
Figure 1: Overall structure of the WD40-deleted Apaf-1 bound to ADP. a, A ribbon diagram of the structure of Apaf-1 (residues 1 -591) bound to ADP. Apaf-1 sequentially comprises five distinct domains: CARD (coloured green), an / fold (blue), helical domain I (cyan), a winged-helix domain (magenta) and helical domain II (red). These five domains pack against one another to generate a relatively compact structure. ADP binds to the hinge region between the / fold and helical domain I but is also coordinated by two critical residues from the winged-helix domain. b, The structure of Apaf-1 in another orientation. Relative to a, Apaf-1 is rotated 90° along a vertical axis within the plane of paper. c, A stereo view showing the binding of ADP in the Apaf-1 structure. The |F[o] - F[c]| omit electron density map, contoured at 2.0 , is calculated with the omission of ADP and shown in red around ADP. Figures 1 -3 and 5 were prepared using MOLSCRIPT29 and GRASP30.

Figure 3.
Figure 3: ADP serves as an organizing centre for the adjoining three domains and locks Apaf-1 in an inactive conformation. a, ADP is deeply buried and inaccessible to even small molecules unless the surrounding domains undergo conformational changes. Left, a cross-section of Apaf-1, with its van der Waals surface represented by a colour-coded mesh. Right, the CARD domain (green) blocks the only solvent channel to the ADP-binding pocket. b, A stereo representation of the coordination of ADP by residues from three domains. As in other AAA + ATPases16, ADP is bound primarily in the hinge region between the / fold (blue) and helical domain I (cyan). In Apaf-1, the winged-helix domain also contributes a direct hydrogen bond (from His 438) to the -phosphate group and a water-mediated hydrogen bond (from Ser 422) to the ribose.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2005, 434, 926-933) copyright 2005.

Figures were selected by an automated process.