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Structure of the Keap1:Nrf2 interface provides mechanistic insight into Nrf2 signaling
Open accessAbstract
Keap1 is a BTB-Kelch substrate adaptor protein that regulates steady-state levels of Nrf2, a bZIP transcription factor, in response to oxidative stress. We have determined the structure of the Kelch domain of Keap1 bound to a 16-mer peptide from Nrf2 containing a highly conserved DxETGE motif. The Nrf2 peptide contains two short antiparallel beta-strands connected by two overlapping type I beta-turns stabilized by the aspartate and threonine residues. The beta-turn region fits into a binding pocket on the top face of the Kelch domain and the glutamate residues form multiple hydrogen bonds with highly conserved residues in Keap1. Mutagenesis experiments confirmed the role of individual amino acids for binding of Nrf2 to Keap1 and for Keap1-mediated repression of Nrf2-dependent gene expression. Our results provide a detailed picture of how a BTB-Kelch substrate adaptor protein binds to its cognate substrate and will enable the rational design of novel chemopreventive agents.
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“Crystal structures of peptide substrate complexes have been reported for four BTB-Kelch family members, including KEAP1, KLHL2, KLHL3 and KLHL20 (refs 80,81,82 ).”
From Targeted protein degradation: expanding the toolbox (2019) · cites this paper as [80]
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Anti-inflammatory Effect of a Cell-Penetrating Peptide Targeting the Nrf2/Keap1 Interaction
Steel, R., Cowan, J., Payerne, E., O'Connell, M. A., & Searcey, M. (2012) · ACS Medicinal Chemistry Letters · doi:10.1021/ml300041g · Cited by 113
Probing the structural requirements of non-electrophilic naphthalene-based Nrf2 activators
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“In crystal structures of a Nrf2 peptide bound to the Kelch domain [55], Glu 79 and Glu 82 of the ETGE motif form ionic interactions with Arg 415 and 483 of Keap1 [55].”
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Herpes Simplex Virus 1-Induced Ferroptosis Contributes to Viral Encephalitis
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“In response to oxidative stress, Nrf2 dissociates from Keap1 and translocates to the nucleus, leading to the increased expression of antioxidant-related genes (10).”
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“This site lies in a “d–a” loop between successive blades of the Kelch propeller; these loops are involved in substrate binding (25).”
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Sova, M., & Saso, L. (2018) · Drug Design Development and Therapy · doi:10.2147/dddt.s172612 · Cited by 104
“The available crystal structures 18,80 of the human Keap1 Kelch domain were also used for an in silico fragment-based approach to discover 1,4-diaryl-1,2,3-triazole inhibitors of the Keap1-Nrf2 PPI.”
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“The FP assay of the N-acetylated 9mer Nrf2 peptides showed similar binding affinities to the longer peptides with Keap1.”
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“Nrf2 belongs to the Cap'n'collar/basic region leucine zipper transcription factor family, which is activated by diverse oxidants, pro-oxidants, antioxidants, chemopreventive agents, and electrophiles [9,10].”
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Allyl-, butyl- and phenylethyl-isothiocyanate activate Nrf2 in cultured fibroblasts
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“In addition, Keap1 mutant H436A demonstrates dramatically decreased affinity for an Neh2-derived peptide and shows no detectable ability to repress Nrf2 in a reporter assay (56).”
BackgroundInfluentialExploring the target scope of KEAP1 E3 ligase-based PROTACs
Du, G., Jiang, J., Henning, N. J., Safaee, N., Koide, E., Nowak, R. P., Donovan, K. A., Yoon, H., You, I., Yue, H., et al. (2022) · Cell chemical biology · doi:10.1016/j.chembiol.2022.08.003 · Cited by 97
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“Thus, occupying the Kelch structural domain of Keap1, which competitively binds to Nrf2, can facilitate Nrf2 entry into the nucleus and initiate downstream antioxidant enzymes [45].”
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“Nrf2 has a very short half-life because of its interaction with the BTB-Kelch protein Keap1, which promotes Nrf2 degradation by the proteasome (Lo et al., 2006).”
BackgroundPterostilbene-mediated Nrf2 activation: Mechanistic insights on Keap1:Nrf2 interface
Bhakkiyalakshmi, E., Kesavan, D. K., Karthik, S., Sireesh, D., Hopper, W., Paulmurugan, R., & Ramkumar, K. M. (2016) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2016.05.011 · Cited by 93
Genomic Structure and Variation of Nuclear Factor (Erythroid-Derived 2)-Like 2
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“F e l i s c a t u s homology (Neh) domains configuring the protein sequence of either species (Table 2), and the potential functions of each region, particularly the highly conserved KEAP1-binding Neh2 and DNA-(ARE-) binding Neh1 domains, have been intensively investigated [12, 14, 15].”
Lucas, X., & Ciulli, A. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.12.015 · Cited by 92
“KEAP1 NRF2 [DNS]x[DES][TNS ]GE 2FLU [76] Compound 7”
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“Nrf2 is a basic leucine zipper transcription factor belonging to the unique subset of Cap N′ Collar transcription factors [3,4] and forms a heterodimer with the ZIP domain of small Maf proteins [5].”
BackgroundTargeting NRF2 to treat cancer
Sivinski, J., Zhang, D. D., & Chapman, E. (2021) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2021.06.003 · Cited by 94
Marburgvirus Hijacks Nrf2-Dependent Pathway by Targeting Nrf2-Negative Regulator Keap1
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“Keap1 is the receptor for a Cul3 ‐ dependent ubiquitin ligase complex that recognizes and targets the transcription activator Nrf2 for degradation 42 .”
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“Several ETGE-containing peptides have been reported to bind Keap1 Kelch domain with varying affinity, and these include the 16mer Nrf2 peptide (residues 69–84), 14mer Nrf2 peptide (residues 74–87), and 10mer Nrf2 peptide (residues 76–85) (38).”
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Recent progress in Keap1-Nrf2 protein-protein interaction inhibitors
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Discovery of Keap1−Nrf2 small−molecule inhibitors from phytochemicals based on molecular docking
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“The 24 candidates bind with the special amino acids on Keap1, such as Ser363, Ser508, Ser555 and Ser602, which have been reported to be the key amino acids in the structure of the Keap1−Nrf2 interface (Lo et al., 2014).”
NRF2 Regulation Processes as a Source of Potential Drug Targets against Neurodegenerative Diseases
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S‐Glutathionylation of Keap1: a new role for glutathioneS‐transferase pi in neuronal protection
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“Each blade is a twisted β-sheet composed of four antiparallel β-strands (A–D): strand A is positioned in line with the central channel and runs almost parallel with the six-fold axis of the propeller, while strands B–D progressively acquire more distance from the central axis and exhibit more twist until almost comple…”
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Defining the functional targets of cap'n'collar transcription factors NRF1, NRF2, and NRF3
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“We introduced a mutation (T80D) in the Neh1 domain of NRF2, which has been reported to inhibit its interactions with KEAP1 and to promote constitutive transcriptional activation [25].”
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“Nrf2 is a precursor for several defensive enzymes and antioxidants used against xenobiotics [6,7].”
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Zhuang, J., Liu, Q., Wu, D., & Tie, L. (2022) · Acta Pharmacologica Sinica · doi:10.1038/s41401-021-00852-9 · Cited by 77
“With the elucidation of the co-crystal structures of Keap1 and Nrf2 peptides, a large number of Keap1-Nrf2 inhibitors targeting their PPI have been reported, including small molecules and peptides [76, 77].”
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“Importantly, mutation of these residues in Keap1 disrupted its ability to bind Nrf2 and repress Nrf2-dependent transcription 25,26 .”
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p62-Dependent Phase Separation of Patient-Derived KEAP1 Mutations and NRF2
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Activation of anti-oxidant Nrf2 signaling by enone analogues of curcumin
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Functional Aspects of Redox Control During Neuroinflammation
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“Keap1 also has an intervening region (IVR) sequence, outside the BTB domain, responsible for the association between Keap1 and the Cullin-based E3-ligase (Cul3), a subunit of the ubiquitin E3 ligase complex, and transfers ubiquitin to Nrf2 protein (153).”
InfluentialZheng, A., Chevalier, N., Calderoni, M., Dubuis, G., Dormond, O., Ziros, P. G., Sykiotis, G., & Widmann, C. (2019) · OncoTarget · doi:10.18632/oncotarget.27361 · Cited by 55
“In our screen, all six sgRNAs targeted the Kelch domain of KEAP1, which is responsible for the binding to Nrf2 [13].”
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“Furthermore, the conserved threonine residue was essential for the structure stabilization of Nrf2 in HEK-293 T cells [77].”
BackgroundStructural and mechanistic insights into the Keap1-Nrf2 system as a route to drug discovery
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NRF2 in human neoplasm: Cancer biology and potential therapeutic target
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Thioredoxin Signaling Pathways in Cancer
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“Keap1 in mammalian cells is a highly cysteine-rich protein, and bridges the cullin3 E3 ubiquitin ligase and Nrf2, leading to the ubiquitination of Nrf2 and subsequent proteasome degradation of Nrf2 (Lo et al, 2006) (Fig.”
Self-citationCRL3s: The BTB-CUL3-RING E3 Ubiquitin Ligases
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“…ID: 6WYD [136]) (Figure 1a), XO in complex with quercetin (PDB ID: 3NVY [137]) (Figure 1b), Keap1 in complex with an Nrf2 peptide (PDB ID: 2FLU [138]) and p47phox in complex with a p22phox peptide (PDB ID: 1WLP [139]) were retrieved from the PDB and the regions of interaction with their…”
MethodInfluentialInduction of Heme Oxygenase I (HMOX1) by HPP-4382: A Novel Modulator of Bach1 Activity
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Richardson, B. G., Jain, A. D., Potteti, H. R., Lazzara, P. R., David, B. P., Tamatam, C. R., Choma, E., Skowron, K. J., Dye, K., Siddiqui, Z., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01133 · Cited by 57
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“The disassociation of Nrf2 from Keap1 may be through the direct modification of reactive cysteine residues in Keap1 by endogenous products of OS or reactive chemicals [12,62,63].”
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Leung, C., Zhang, J.-T., Yang, G., Liu, H., Han, Q., & Ma, D. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20184445 · Cited by 54
“Human Keap1 has five domains: the N-terminal region (NTR), the broad-complex, tramtrack and bric a brac (BTB) domain, an intervening region (IVR) with a double glycine region (DGR), multiple cysteines, and a C-terminal region (CTR) [26].”
BackgroundBinding thermodynamics and kinetics guided optimization of potent Keap1–Nrf2 peptide inhibitors
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Recent progress in the development of small molecule Nrf2 activators: a patent review (2017-present)
Zhou, H.-S., Wang, Y., You, Q., & Jiang, Z. (2020) · Expert Opinion on Therapeutic Patents · doi:10.1080/13543776.2020.1715365 · Cited by 53
“Human Keap1 contains five domains: N-terminal domain (NTD, 1–60); Broad complex, Tramtrack, and Bric- ́a-Brac (BTB, 61–178) domain; intervening region (IVR, 179–321); double glycine repeat (DGR, 322–608) and Kelch domain; and C-terminal region (CTR, 609–625) [20,21].”
BackgroundBayındır, Z. S., Losada‐Barreiro, S., Bravo‐Díaz, C., Sova, M., Kristl, J., & Saso, L. (2021) · Antioxidants · doi:10.3390/antiox10050685 · Cited by 58
Nrf2, the Major Regulator of the Cellular Oxidative Stress Response, is Partially Disordered
Karunatilleke, N. C., Fast, C. S., Ngo, V., Brickenden, A. M., Duennwald, M. L., Konermann, L., & Choy, W. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147434 · Cited by 52
“Nrf2 activity is regulated through the interactions with a suite of different proteins [4,21–27], including Kelch-like ECH-associated protein 1 (Keap1) [22,28].”
BackgroundInfluentialExploring the links between polyphenols, Nrf2, and diabetes: A review
Ebrahimi, R., Mohammadpour, A., Medoro, A., Davinelli, S., Saso, L., & Miroliaei, M. (2025) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2025.118020 · Cited by 61
Metadata
- Authors
- Lo, S., Li, X., Henzl, M. T., Beamer, L. J., & Hannink, M.
- Affiliations
- University of Missouri (US)
- Corresponding author
- Beamer, Lesa J
- Hannink, Mark
- Venue
- The EMBO Journal
- Published
- 2006-08-03
- Volume
- 25
- Issue
- 15
- Pages
- 3605-3617
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC1538563
- OpenAlex
- W2141982524
- Cited by
- 604
- References
- 68
- Citations by year
- 2026: 66 · 2025: 66 · 2024: 44 · 2023: 48 · 2022: 47 · 2021: 36 · 2020: 35 · 2019: 23 · 2018: 22 · 2017: 21 · 2016: 25 · 2015: 25 · 2014: 22 · 2013: 34 · 2012: 22
- FWCI
- 4.63
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- The EMBO Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (P50CA103130)
- National Center for Complementary and Integrative Health (AT003899, R01AT003899)
- Lawrence Berkeley National Laboratory
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics, phytochemicals, and oxidative stress
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Redox biology and oxidative stress
- Keywords
- Keap1, Nrf2, Kelch domain, protein-protein interaction, beta-turn, oxidative stress response, chemoprevention, protein structure
- MeSH terms
- Kelch-Like ECH-Associated Protein 1, Amino Acid Sequence, Animals, Binding Sites, Cells, Cultured, Chlorocebus aethiops, Humans, Models, Molecular, Molecular Sequence Data, Phosphorylation, Protein Binding, Protein Conformation, Signal Transduction, Conserved Sequence, Protein Structure, Tertiary, Dimerization, COS Cells, Amino Acid Motifs, Intracellular Signaling Peptides and Proteins, NF-E2-Related Factor 2
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