7K2A

Kelch domain of human KEAP1 bound to Nrf2 peptide, LDEETGEFA

DOI: 10.2210/pdb7K2A/pdb

Classification: PROTEIN BINDING/Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-08 Released: 2021-04-07
Deposition Author(s): Muellers, S.N., Allen, K.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.244
R-Value Work: 0.210
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning.

Ortet, P.C., Muellers, S.N., Viarengo-Baker, L.A., Streu, K., Szymczyna, B.R., Beeler, A.B., Allen, K.N., Whitty, A.

(2021) J Am Chem Soc 143: 3779-3793

PubMed: 33683866 Search on PubMed
DOI: 10.1021/jacs.0c09799
Primary Citation of Related Structures:
7K28, 7K29, 7K2P, 7K2Q, 7K2N, 7K2O, 7K2R, 7K2S, 7K2H, 7K2I

PubMed Abstract:

Macrocycles, including macrocyclic peptides, have shown promise for targeting challenging protein-protein interactions (PPIs). One PPI of high interest is between Kelch-like ECH-Associated Protein-1 (KEAP1) and Nuclear Factor (Erythroid-derived 2)-like 2 (Nrf2). Guided by X-ray crystallography, NMR, modeling, and machine learning, we show that the full 20 nM binding affinity of Nrf2 for KEAP1 can be recapitulated in a cyclic 7-mer peptide, c[( D )-β-homoAla-DPETGE]. This compound was identified from the Nrf2-derived linear peptide GDEETGE ( K _D = 4.3 μM) solely by optimizing the conformation of the cyclic compound, without changing any KEAP1 interacting residue. X-ray crystal structures were determined for each linear and cyclic peptide variant bound to KEAP1. Despite large variations in affinity, no obvious differences in the conformation of the peptide binding residues or in the interactions they made with KEAP1 were observed. However, analysis of the X-ray structures by machine learning showed that locations of strain in the bound ligand could be identified through patterns of subangstrom distortions from the geometry observed for unstrained linear peptides. We show that optimizing the cyclic peptide affinity was driven partly through conformational preorganization associated with a proline substitution at position 78 and with the geometry of the noninteracting residue Asp77 and partly by decreasing strain in the ETGE motif itself. This approach may have utility in dissecting the trade-off between conformational preorganization and strain in other ligand-receptor systems. We also identify a pair of conserved hydrophobic residues flanking the core DxETGE motif which play a conformational role in facilitating the high-affinity binding of Nrf2 to KEAP1.

Organizational Affiliation:

Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary. Electronic address: ambrus.attila@med.semmelweis-univ.hu.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A, B	301	Homo sapiens	Mutation(s): 0 Gene Names: KEAP1, INRF2, KIAA0132, KLHL19
Find proteins for Q14145 (Homo sapiens) Explore Q14145 Go to UniProtKB: Q14145
NIH Common Fund Data Resources
PHAROS: Q14145 GTEx: ENSG00000079999
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-LEU-ASP-GLU-GLU-THR-GLY-GLU-PHE-ALA-NH2	P	11	Homo sapiens	Mutation(s): 0
Protein Feature View Expand
Reference Sequence