3G76

Crystal structure of XIAP-BIR3 in complex with a bivalent compound

Summary for 3G76

• Entry DOI: 10.2210/pdb3g76/pdb
• Related: 1G73 2JK7 3EYL
• Descriptor: Baculoviral IAP repeat-containing protein 4, ZINC ION, 1,1'-{hexa-2,4-diyne-1,6-diylbis[oxy{(2S,3R)-2-[(N-methyl-L-alanyl)amino]-1-oxobutane-3,1-diyl}(2S)pyrrolidine-1,2-diylmethanediyl]}bis[5-(phenylsulfanyl)-1H-tetrazole], ... (4 entities in total)
• Functional Keywords: apoptosis, iap, smacdiablo, peptidomimetics, pro-apoptotic drugs, cytoplasm, ligase, metal-binding, phosphoprotein, polymorphism, protease inhibitor, thiol protease inhibitor, ubl conjugation, ubl conjugation pathway, zinc, zinc-finger
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: P98170
• Total number of polymer chains: 8
• Total formula weight: 121257.88

Authors

Cossu, F.,Milani, M.,Mastrangelo, E.,Bolognesi, M. (deposition date: 2009-02-09, release date: 2009-05-12, Last modification date: 2023-11-01)

Primary citation

Cossu, F.,Milani, M.,Mastrangelo, E.,Vachette, P.,Servida, F.,Lecis, D.,Canevari, G.,Delia, D.,Drago, C.,Rizzo, V.,Manzoni, L.,Seneci, P.,Scolastico, C.,Bolognesi, M.
Structural basis for bivalent smac-mimetics recognition in the IAP protein family
J.Mol.Biol., 392:630-644, 2009

PubMed Abstract: XIAP is an apoptotic regulator protein that binds to the effector caspases -3 and -7 through its BIR2 domain, and to initiator caspase-9 through its BIR3 domain. Molecular docking studies suggested that Smac-DIABLO may antagonize XIAP by concurrently targeting both BIR2 and BIR3 domains; on this basis bivalent Smac-mimetic compounds have been proposed and characterized. Here, we report the X-ray crystal structure of XIAP-BIR3 domain in complex with a two-headed compound (compound 3) with improved efficacy relative to its monomeric form. A small-angle X-ray scattering study of XIAP-BIR2BIR3, together with fluorescence polarization binding assays and compound 3 cytotoxicity tests on HL60 leukemia cell line are also reported. The crystal structure analysis reveals a network of interactions supporting XIAP-BIR3/compound 3 recognition; moreover, analytical gel-filtration chromatography shows that compound 3 forms a 1:1 stoichiometric complex with a XIAP protein construct containing both BIR2 and BIR3 domains. On the basis of the crystal structure and small-angle X-ray scattering, a model of the same BIR2-BIR3 construct bound to compound 3 is proposed, shedding light on the ability of compound 3 to relieve XIAP inhibitory effects on caspase-9 as well as caspases -3 and -7. A molecular modeling/docking analysis of compound 3 bound to cIAP1-BIR3 domain is presented, considering that Smac-mimetics have been shown to kill tumor cells by inducing cIAP1 and cIAP2 ubiquitination and degradation. Taken together, the results reported here provide a rationale for further development of compound 3 as a lead in the design of dimeric Smac mimetics for cancer treatment.

PubMed: 19393243
DOI: 10.1016/j.jmb.2009.04.033

Experimental method

X-RAY DIFFRACTION (3 Å)