3LNZ

Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant)

Summary for 3LNZ

• Entry DOI: 10.2210/pdb3lnz/pdb
• Related: 1YCR 3EQS 3IUX 3LNJ 3LO1 3LO2 3LO4 3LO9 3LOE
• Descriptor: E3 ubiquitin-protein ligase Mdm2, 12-mer peptide inhibitor, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: p53-binding protein of mdm2, oncoprotein mdm2, human double minute 2 protein, hdm2, mdm2-peptide inhibitor complex, p53 peptide activator n8a-pmi, host-virus interaction, ligase, metal-binding, nucleus, phosphoprotein, proto-oncogene, ubl conjugation pathway, zinc-finger, ligase-ligase inhibitor complex, ligase/ligase inhibitor
• Cellular location: Nucleus, nucleoplasm: Q00987
• Total number of polymer chains: 16
• Total formula weight: 91718.99

Authors

Pazgier, M.,Lu, W. (deposition date: 2010-02-03, release date: 2010-03-09, Last modification date: 2023-09-06)

Primary citation

Li, C.,Pazgier, M.,Li, C.,Yuan, W.,Liu, M.,Wei, G.,Lu, W.Y.,Lu, W.
Systematic mutational analysis of peptide inhibition of the p53-MDM2/MDMX interactions.
J.Mol.Biol., 398:200-213, 2010

PubMed Abstract: Inhibition of the interaction between the tumor suppressor protein p53 and its negative regulators MDM2 and MDMX is of great interest in cancer biology and drug design. We previously reported a potent duodecimal peptide inhibitor, termed PMI (TSFAEYWNLLSP), of the p53-MDM2 and -MDMX interactions. PMI competes with p53 for MDM2 and MDMX binding at an affinity roughly 2 orders of magnitude higher than that of (17-28)p53 (ETFSDLWKLLPE) of the same length; both peptides adopt nearly identical alpha-helical conformations in the complexes, where the three highlighted hydrophobic residues Phe, Trp, and Leu dominate PMI or (17-28)p53 binding to MDM2 and MDMX. To elucidate the molecular determinants for PMI activity and specificity, we performed a systematic Ala scanning mutational analysis of PMI and (17-28)p53. The binding affinities for MDM2 and MDMX of a total of 35 peptides including 10 truncation analogs were quantified, affording a complete dissection of energetic contributions of individual residues of PMI and (17-28)p53 to MDM2 and MDMX association. Importantly, the N8A mutation turned PMI into the most potent dual-specific antagonist of MDM2 and MDMX reported to date, registering respective K(d) values of 490 pM and 2.4 nM. The co-crystal structure of N8A-PMI-(25-109)MDM2 was determined at 1.95 A, affirming that high-affinity peptide binding to MDM2/MDMX necessitates, in addition to optimized intermolecular interactions, enhanced helix stability or propensity contributed by non-contact residues. The powerful empirical binding data and crystal structures present a unique opportunity for computational studies of peptide inhibition of the p53-MDM2/MDMX interactions.

PubMed: 20226197
DOI: 10.1016/j.jmb.2010.03.005

Experimental method

X-RAY DIFFRACTION (1.95 Å)