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Binding of peptide mimicking the ETGE loop of dipeptidyl peptidase III to the Kelch domain of Keap1

Signaling pathway of the NRF2 ̶ KEAP1 factor 2 (nuclear factor erythroid 2-related–Kelch like ECH- associated protein 1) is important for cell protection. However, it is impaired in many cancer cells where NRF2 target gene expression leads to resistance to chemotherapeutic drugs. Dipeptidyl peptidase III (DPP III) competitively binds to KEAP1 in the conditions of oxidative stress and induces release of NRF2 and its translocation into nucleus. The binding is established mainly through the ETGE motif located on the flexible loop of DPP III and the Kelch domain of KEAP1. To better understand interactions between DPP III and the Kelch domain of the KEAP1 protein we solved its crystal structure at a resolution of 2.70 Å (Figure 1A). The asymmetric unit contains one protein molecule, one 11-mer peptide molecule mimicking the ETGE loop of the DPP III peptide, nine water molecules, and one sodium ion. The final model was refined to Rwork = 18.1% and Rfree = 25.8%. Clear electron density (Figure 1B) was observed in the difference map near the region involved in the interactions with the ETGE motif, allowing proper fitting of the peptide and determination of the main interactions between the peptide and the Kelch domain of the KEAP1 protein. We found that ETGE itself is firmly attached to the peptide by strong hydrogen bonds in the same way as in the crystal structure of the Kelch–NRF2 complex. The backbone of the 11 AA peptide makes five hydrogen bonds with the Kelch domain, in four of them the peptide residues (P479, E480, T481 and Q484) are hydrogen bond acceptors, and donor in one (Q484).

Kelch domain ; ETGE loop ; crystal structure

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