2VSL

Crystal Structure of XIAP BIR3 with a Bivalent Smac Mimetic

Summary for 2VSL

• Entry DOI: 10.2210/pdb2vsl/pdb
• Related: 1C9Q 1F9X 1G3F 1G73 1I3O 1I4O 1I51 1KMC 1NW9 1TFQ 1TFT 2JK7
• Descriptor: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4, PEPTIDE (MAA-LYS-PRO-PHE), POLYETHYLENE GLYCOL (N=34), ... (5 entities in total)
• Functional Keywords: zinc-finger, polymorphism, smac mimetic, metal-binding, ubl conjugation pathway, thiol protease inhibitor, phosphoprotein, ubl conjugation, protease inhibitor, bir3, zinc, xiap, ligase, apoptosis, cytoplasm, hydrolase inhibitor
• Biological source: HOMO SAPIENS (HUMAN); More
• Cellular location: Cytoplasm: P98170
• Total number of polymer chains: 2
• Total formula weight: 13161.22

Authors

Meagher, J.L.,Stuckey, J.A. (deposition date: 2008-04-24, release date: 2008-09-02, Last modification date: 2024-11-13)

Primary citation

Nikolovska-Coleska, Z.,Meagher, J.L.,Jiang, S.,Yang, C.Y.,Qiu, S.,Roller, P.P.,Stuckey, J.A.,Wang, S.
Interaction of a Cyclic, Bivalent Smac Mimetic with the X-Linked Inhibitor of Apoptosis Protein.
Biochemistry, 47:9811-, 2008

PubMed Abstract: We have designed and synthesized a cyclic, bivalent Smac mimetic (compound 3) and characterized its interaction with the X-linked inhibitor of apoptosis protein (XIAP). Compound 3 binds to XIAP containing both BIR2 and BIR3 domains with a biphasic dose-response curve representing two binding sites with IC 50 values of 0.5 and 406 nM, respectively. Compound 3 binds to XIAPs containing the BIR3-only and BIR2-only domain with K i values of 4 nM and 4.4 microM, respectively. Gel filtration experiments using wild-type and mutated XIAPs showed that 3 forms a 1:2 stoichiometric complex with XIAP containing the BIR3-only domain. However, it forms a 1:1 stoichiometric complex with XIAP containing both BIR2 and BIR3 domains, and both BIR domains are involved in the binding. Compound 3 efficiently antagonizes inhibition of XIAP in a cell-free functional assay and is >200 times more potent than its corresponding monovalent compound 2. Determination of the crystal structure of 3 in complex with the XIAP BIR3 domain confirms that 3 induces homodimerization of the XIAP BIR3 domain and provides a structural basis for the cooperative binding of one molecule of compound 3 to two XIAP BIR3 molecules. On the basis of this crystal structure, a binding model of XIAP containing both BIR2 and BIR3 domains and 3 was constructed, which sheds light on the ability of 3 to relieve the inhibition of XIAP with not only caspase-9 but also caspase-3/-7. Compound 3 is cell-permeable, effectively activates caspases in whole cells, and potently inhibits cancer cell growth. Compound 3 is a useful biochemical and pharmacological tool for further elucidating the role of XIAP in regulation of apoptosis and represents a promising lead compound for the design of potent, cell-permeable Smac mimetics for cancer treatment.

PubMed: 18717598
DOI: 10.1021/BI800785Y

Experimental method

X-RAY DIFFRACTION (2.1 Å)