title: Computational Analysis of the Ligand Binding Site of the Extracellular ATP Receptor, DORN1.
abstract: DORN1 (also known as P2K1) is a plant receptor for extracellular ATP, which belongs to a large gene family of legume-type (L-type) lectin receptor kinases. Extracellular ATP binds to DORN1 with strong affinity through its lectin domain, and the binding triggers a variety of intracellular activities in response to biotic and abiotic stresses. However, information on the tertiary structure of the ligand binding site of DORN1is lacking, which hampers efforts to fully elucidate the mechanism of receptor action. Available data of the crystal structures from more than 50 L-type lectins enable us to perform an in silico study of molecular interaction between DORN1 and ATP. In this study, we employed a computational approach to develop a tertiary structure model of the DORN1 lectin domain. A blind docking analysis demonstrated that ATP binds to a cavity made by four loops (defined as loops A B, C and D) of the DORN1 lectin domain with high affinity. In silico target docking of ATP to the DORN1 binding site predicted interaction with 12 residues, located on the four loops, via hydrogen bonds and hydrophobic interactions. The ATP binding pocket is structurally similar in location to the carbohydrate binding pocket of the canonical L-type lectins. However, four of the residues predicted to interact with ATP are not conserved between DORN1 and the other carbohydrate-binding lectins, suggesting that diversifying selection acting on these key residues may have led to the ATP binding activity of DORN1. The in silico model was validated by in vitro ATP binding assays using the purified extracellular lectin domain of wild-type DORN1, as well as mutated DORN1 lacking key ATP binding residues.
authors: Division of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri Columbia, Missouri, 65211, United States of America.
authors: Cuong The
authors: http://orcid.org/0000-0002-8700-9598
authors: CT
authors: Nguyen
authors: Department of Plant Pathology, Washington State University, Pullman, Washington, 646430, United States of America.
authors: Kiwamu
authors: http://orcid.org/0000-0001-5045-560X
authors: K
authors: Tanaka
authors: Division of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri Columbia, Missouri, 65211, United States of America.
authors: Yangrong
authors: Y
authors: Cao
authors: Division of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri Columbia, Missouri, 65211, United States of America.
authors: Sung-Hwan
authors: SH
authors: Cho
authors: Department of Computer Science, Informatics Institute, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, United States of America.
authors: Dong
authors: D
authors: Xu
authors: Division of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri Columbia, Missouri, 65211, United States of America.
authors: Gary
authors: G
authors: Stacey
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D037102:Lectins / Q000378:metabolism; D008024:Ligands; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D018048:Receptors, Purinergic P2 / Q000737:chemistry / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
chemical_list: D037102:Lectins; D008024:Ligands; D018048:Receptors, Purinergic P2