title: The 3D structure of the defense-related rice protein Pir7b predicted by homology modeling and ligand binding studies.
abstract: To better understand the ligand-binding mechanism of protein Pir7b, important part in detoxification of a pathogen-derived compound against Pyricularia oryzae, a 3D structure model of protein Pir7b was constructed based on the structure of the template SABP2. Three substrates were docking to this protein, two of them were proved to be active, and some critical residues are identified, which had not been confirmed by the experiments. His87 and Leu17 considered as 'oxyanion hole' contribute to initiating the Ser86 nucleophilic attack. Gln187 and Asp139 can form hydrogen bonds with the anilid group to maintain the active binding orientation with the substrates. The docking model can well interpret the specificity of protein Pir7b towards the anilid moiety of the substrates and provide valuable structure information about the ligand binding to protein Pir7b.
authors.affiliation: State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China.
authors.forename: Quan
authors.initials: Q
authors.lastname: Luo
authors.forename: Wei-Wei
authors.initials: WW
authors.lastname: Han
authors.forename: Yi-Han
authors.initials: YH
authors.lastname: Zhou
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yao
authors.forename: Ze-Sheng
authors.initials: ZS
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D004950:Esterases / Q000737:chemistry*; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009284:Naphthols; D012275:Oryza / Q000737:chemistry*; D010940:Plant Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D055672:Static Electricity; D040681:Structural Homology, Protein; D013816:Thermodynamics
chemical_list: D008024:Ligands; D009284:Naphthols; D010940:Plant Proteins; D004950:Esterases; C113255:Pir7B protein, Oryza sativa