Crystal structure of DRIK1, a stress-responsive receptor-like pseudokinase, reveals the molecular basis for the absence of ATP binding

Abstract

Background: Plants reprogram metabolism and development to rapidly adapt to biotic and abiotic stress. Protein kinases play a significant role in this process by phosphorylating protein substrates that activate or inactivate signaling cascades that regulate cellular and metabolic adaptations. Despite their importance in plant biology, a notably small fraction of the plant kinomes has been studied to date. Results: In this report, we describe ZmDRIK1, a stress-responsive receptor-like pseudokinase whose expression is downregulated under water restriction. We show the structural features and molecular basis of the absence of ATP binding exhibited by ZmDRIK1. The ZmDRIK1 kinase domain lacks conserved amino acids that are essential for phosphorylation activity. The crystal structure of the ZmDRIK1 kinase domain revealed the presence of a spine formed by the side chain of the triad Leu 240 , Tyr 363 , and Leu 375 that occludes the ATP binding pocket. Although ZmDRIK1 is unable to bind nucleotides, it does bind the small molecule ENMD-2076 which, in a cocrystal structure, revealed the potential to serve as a ZmDRIK1 inhibitor.Conclusion: ZmDRIK1 is a novel receptor-like pseudokinase responsive to biotic and abiotic stress. The absence of ATP binding and consequently, the absence of phosphorylation activity, was proven by the crystal structure of the apo form of the protein kinase domain. The expression profiling of the gene encoding ZmDRIK1 suggests this kinase may play a role in downregulating the expression of stress responsive genes that are not necessary under normal conditions. Under biotic and abiotic stress, ZmDRIK1 is down-regulated to release the expression of these stress-responsive genes.

OsSRF8 interacts with OsINP1 and OsDAF1 to regulate pollen aperture formation in rice

“…Previous studies have demonstrated that Arabidopsis-derived STRUBBELIG ( SUB ) is classified within the SRF family and encodes an atypical kinase, often referred to as a pseudokinase due to the absence of one or more key residues essential for phosphoryl transfer 39 , 45 – 47 . Sequence alignment revealed that like SUB, OsSRF8 harbors amino acid alterations in the conserved positions crucial for kinase activity, such as E474M in the C-helix, D556N in the HRD motif, and D574H in the DFG motif (Supplementary Fig.…”

Exploring the Potential of Vortioxetine Derivatives as Inhibitors of SARS‐CoV‐2 Main Protease: A Computational Study

“…Subsequently, energy optimization was carried out using 2500 steps of steepest descent method and 2500 steps of conjugate gradient method. The system was then subject to 100 ps of NVT ensemble simulation and 100 ps of NPT equilibrium simulation under the condition of maintaining a temperature of 298.15 K. Finally, a 100 ns NPT ensemble simulation was performed under periodic boundary conditions, calculating long‐range electrostatic interactions using the PME method, a non‐bonded cut‐off distance set to 1 nm, a collision frequency set to 2 ps, system pressure of 101.325 kPa, integration step of 2 s and trajectory saved every 10 ps [31,32] …”

“…The system was then subject to 100 ps of NVT ensemble simulation and 100 ps of NPT equilibrium simulation under the condition of maintaining a temperature of 298.15 K. Finally, a 100 ns NPT ensemble simulation was performed under periodic boundary conditions, calculating long-range electrostatic interactions using the PME method, a non-bonded cut-off distance set to 1 nm, a collision frequency set to 2 ps, system pressure of 101.325 kPa, integration step of 2 s and trajectory saved every 10 ps. [31,32] Using molecular dynamics simulation, the binding free energy between a protein and a molecule was calculated. This calculation enables a deeper understanding of their interaction mechanism, which can contribute to drug design and treatment.…”