title: Structure of the apoptotic protease-activating factor 1 bound to ADP.
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.
authors.affiliation: Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey 08544, USA.
authors.forename: Stefan J
authors.initials: SJ
authors.lastname: Riedl
authors.forename: Wenyu
authors.initials: W
authors.lastname: Li
authors.forename: Yang
authors.initials: Y
authors.lastname: Chao
authors.forename: Robert
authors.initials: R
authors.lastname: Schwarzenbacher
authors.forename: Yigong
authors.initials: Y
authors.lastname: Shi
mesh_terms: D000244:Adenosine Diphosphate / Q000378:metabolism*; D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D020816:Amino Acid Motifs; D017209:Apoptosis; D053477:Apoptotic Protease-Activating Factor 1; D001665:Binding Sites; D053453:Caspase 9; D020169:Caspases / Q000378:metabolism; D018360:Crystallography, X-Ray; D045304:Cytochromes c / Q000378:metabolism; D004789:Enzyme Activation; D006868:Hydrolysis; D008954:Models, Biological; D008958:Models, Molecular; D011485:Protein Binding; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017384:Sequence Deletion / Q000235:genetics; D013329:Structure-Activity Relationship
chemical_list: D053477:Apoptotic Protease-Activating Factor 1; D011506:Proteins; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; D045304:Cytochromes c; D053453:Caspase 9; D020169:Caspases; D000251:Adenosine Triphosphatases