Crystal structure of DRIK1, a stress-responsive receptor-like pseudokinase, reveals the molecular basis for the absence of ATP binding
Open Access
- 15 April 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Plant Biology
- Vol. 20 (1), 1-15
- https://doi.org/10.1186/s12870-020-2328-3
Abstract
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. 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 Leu240, Tyr363, and Leu375 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. 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.Keywords
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Funding Information
- FAPESP (2017/19609-6, 2018/06442-9, 2016/23218-0, 2014/50897-0)
This publication has 87 references indexed in Scilit:
- Identification of PAN2 by Quantitative Proteomics as a Leucine-Rich Repeat–Receptor-Like Kinase Acting Upstream of PAN1 to Polarize Cell Division in MaizeTHE PLANT CELL ONLINE, 2012
- A Plasma Membrane Receptor Kinase, GHR1, Mediates Abscisic Acid- and Hydrogen Peroxide-Regulated Stomatal Movement in ArabidopsisTHE PLANT CELL ONLINE, 2012
- A Conserved Non-canonical Motif in the Pseudoactive Site of the ROP5 Pseudokinase Domain Mediates Its Effect on Toxoplasma VirulenceOnline Journal of Public Health Informatics, 2011
- Biochemical, Proteomic, Structural, and Thermodynamic Characterizations of Integrin-linked Kinase (ILK)Online Journal of Public Health Informatics, 2011
- High-throughput production of human proteins for crystallization: The SGC experienceJournal of Structural Biology, 2010
- A Conserved Threonine Residue in the Juxtamembrane Domain of the XA21 Pattern Recognition Receptor Is Critical for Kinase Autophosphorylation and XA21-mediated Immunity*Online Journal of Public Health Informatics, 2010
- Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3Proceedings of the National Academy of Sciences of the United States of America, 2009
- Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle GenesPlant Physiology, 2009
- Phasercrystallographic softwareJournal of Applied Crystallography, 2007
- Multiple Sequence Alignment Using ClustalW and ClustalXCurrent Protocols in Bioinformatics, 2002