PDBsum entry 2vsl

Ligase

PDB id: 2vsl

Contents

Protein chain

96 a.a. *

Ligands

MAA-LYS-PRO-PHE

15P

Metals

_ZN

Waters ×60

* Residue conservation analysis

PDB id:

2vsl

Name:

Ligase

Title:

Crystal structure of xiap bir3 with a bivalent smac mimetic

Structure:

Baculoviral iap repeat-containing protein 4. Chain: a. Fragment: bir3 domain, residues 250-345. Synonym: xiap, e3 ubiquitin-protein ligase xiap, inhibitor of apoptosis protein 3, x- linked inhibitor of apoptosis protein, x- linked iap, iap-like protein, hilp. Engineered: yes. Peptide (maa-lys-pro-phe). Chain: b.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

2.10Å R-factor: 0.218 R-free: 0.226

Authors:

J.L.Meagher,J.A.Stuckey

Key ref:

Z.Nikolovska-Coleska et al. (2008). Interaction of a cyclic, bivalent smac mimetic with the x-linked inhibitor of apoptosis protein. Biochemistry, 47, 9811-9824. PubMed id: 18717598

Date:

24-Apr-08 Release date: 02-Sep-08

Protein chain

P98170  (XIAP_HUMAN) -  E3 ubiquitin-protein ligase XIAP from Homo sapiens

Seq: 497 a.a.

Struc: 96 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

Biochemistry 47:9811-9824 (2008)

PubMed id: 18717598

Interaction of a cyclic, bivalent smac mimetic with the x-linked inhibitor of apoptosis protein.

Z.Nikolovska-Coleska, J.L.Meagher, S.Jiang, C.Y.Yang, S.Qiu, P.P.Roller, J.A.Stuckey, S.Wang.

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.