title: Identification, characterization and structure analysis of a type I ribosome-inactivating protein from Sapium sebiferum (Euphorbiaceae).
abstract: Ribosome-inactivating proteins (RIPs) are N-glycosidases (EC3.2.2.22) that universally inactivate the ribosome, thereby inhibiting protein biosynthesis. In this study, a novel type I RIPs named SEBIN was identified in Sapium sebiferum. Nuclear acid depurine experiment showed that SEBIN had rRNA N-Glycosidase activity. Further experiment indicated that SEBIN significantly inhibited Caenorhabditis elegans development as well as resulted in worm cell apoptosis. This is the first report to evaluate RIPs toxicity using C. elegans. We proposed that SEBIN may impaire C. elegans reproduction in a DNA-damage manner besides traditional protein synthesis inhibition approach. The predicted 3D structure was modeled using threading and ab initio modeling, and the r-RNA binding residue of SEBIN was identified through the protein-ligand docking approach. It showed the amino acid residues, Glu195, Asn81, Ala82, Tyr83, Glu164, Ser163, Ile159 and Arg167, played critical roles in catalytic process. Our results provided the theoretical foundation of structure-function relationships between enzymatic properties, toxicity and structural characterization of SEBIN.
authors.affiliation: Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, PR China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, PR China; College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, Henan, PR China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, PR China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, PR China.
authors.forename: Yingji
authors.initials: Y
authors.lastname: Mao
authors.affiliation: Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, PR China.
authors.forename: Shan
authors.initials: S
authors.lastname: Jin
authors.affiliation: Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, PR China.
authors.forename: Jinyan
authors.initials: J
authors.lastname: Hou
authors.affiliation: Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, PR China.
authors.forename: Hua
authors.initials: H
authors.lastname: Du
authors.affiliation: Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, PR China. Electronic address: yml888@mail.ustc.edu.cn.
authors.forename: Minglei
authors.initials: M
authors.lastname: Yang
authors.affiliation: Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, PR China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, PR China. Electronic address: lfwu@ipp.ac.cn.
authors.forename: Lifang
authors.initials: L
authors.lastname: Wu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017173:Caenorhabditis elegans / Q000187:drug effects / Q000254:growth & development; D003001:Cloning, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics / Q000494:pharmacology; D011487:Protein Conformation; D054788:Ribosome Inactivating Proteins / Q000737:chemistry* / Q000235:genetics / Q000494:pharmacology; D031287:Sapium / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid
chemical_list: D010940:Plant Proteins; D054788:Ribosome Inactivating Proteins
keywords: 3D structure analysis; Caenorhabditis elegans; DNA-damage; Ribosome-inactivating proteins; Sapium sebiferum