title: Novel α-L-arabinofuranosidase from Cellulomonas fimi ATCC 484 and its substrate-specificity analysis with the aid of computer.
abstract: In the process of gene mining for novel α-L-arabinofuranosidases (AFs), the gene Celf_3321 from Cellulomonas fimi ATCC 484 encodes an AF, termed as AbfCelf, with potent activity, 19.4 U/mg under the optimum condition, pH 6.0 and 40 °C. AbfCelf can hydrolyze α-1,5-linked oligosaccharides, sugar beet arabinan, linear 1,5-α-arabinan, and wheat flour arabinoxylan, which is partly different from some previously well-characterized GH 51 AFs. The traditional substrate-specificity analysis for AFs is labor-consuming and money costing, because the substrates include over 30 kinds of various 4-nitrophenol (PNP)-glycosides, oligosaccharides, and polysaccharides. Hence, a preliminary structure and mechanism based method was applied for substrate-specificity analysis. The binding energy (ΔG, kcal/mol) obtained by docking suggested the reaction possibility and coincided with the experimental results. AbfA crystal 1QW9 was used to test the rationality of docking method in simulating the interaction between enzyme and substrate, as well the credibility of the substrate-specificity analysis method in silico.
authors: †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China.
authors: Ying
authors: Y
authors: Yang
authors: †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China.
authors: Lujia
authors: L
authors: Zhang
authors: †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China.
authors: Mingrong
authors: M
authors: Guo
authors: †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China.
authors: Jiaqi
authors: J
authors: Sun
authors: §Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan.
authors: Shingo
authors: S
authors: Matsukawa
authors: †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China.|‡Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, People's Republic of China.
authors: Jingli
authors: J
authors: Xie
authors: †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China.|‡Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, People's Republic of China.
authors: Dongzhi
authors: D
authors: Wei
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D040143:Cellulomonas / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D003001:Cloning, Molecular; D019295:Computational Biology; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D009844:Oligosaccharides / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D013379:Substrate Specificity; D014990:Xylans / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D009844:Oligosaccharides; D014990:Xylans; C085118:arabinoxylan; D006026:Glycoside Hydrolases; C019713:alpha-N-arabinofuranosidase
keywords: binding energy; docking; substrate specificity; α-l-arabinofuranosidase