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.
References
Nov 3, 1993·Carbohydrate Research·F J KormelinkA G Voragen
Sep 15, 1995·Structure·G Davies, B Henrissat
Aug 20, 1996·Biochemistry·J SakonP A Karplus
Apr 1, 2000·Applied and Environmental Microbiology·T DebecheM J O'Donohue
Dec 15, 2000·Plant Physiology·B Henrissat, G J Davies
Oct 24, 2001·Biochemistry·T E GottschalkB Svensson
Nov 9, 2002·Carbohydrate Research·Estelle BonninJean-François Thibault
Dec 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ross I BrinkworthBostjan Kobe
Jan 14, 2003·Journal of Biotechnology·Giuliano DegrassiVittorio Venturi
Jun 26, 2003·Nucleic Acids Research·Torsten SchwedeManuel C Peitsch
Oct 1, 2003·The EMBO Journal·Klaus HövelDietmar Schomburg
Oct 11, 2003·Biotechnology Advances·B C Saha
Jan 13, 2004·Science·Mireia Garcia-VilocaDonald G Truhlar
Dec 14, 2004·Angewandte Chemie·Dudley H WilliamsMin Zhou
Jun 18, 2005·Bioinformatics·H M Garay-MalpartidaJ E Belizário
Nov 23, 2005·Bioinformatics·Konstantin ArnoldTorsten Schwede
Dec 31, 2005·Journal of Industrial Microbiology & Biotechnology·Mondher Th Numan, Narayan B Bhosle
Mar 16, 2007·Applied Microbiology and Biotechnology·Sabriye CanakciNurettin Yayli
Mar 20, 2008·Applied Biochemistry and Biotechnology·Jirawan ApiraksakornRobert E Levin
Jun 14, 2008·Mycological Research·Macarena FritzJaime Eyzaguirre
Apr 29, 2009·Journal of Computational Chemistry·Garrett M MorrisArthur J Olson
Aug 24, 2010·Biotechnology Letters·Guimin ZhangYanhe Ma
Feb 10, 2011·Standards in Genomic Sciences·Birte AbtHans-Peter Klenk
Jul 12, 2012·Journal of Biotechnology·Giulia GonnelliYves Dehouck
Aug 9, 2013·Bioscience, Biotechnology, and Biochemistry·Hirokazu SuzukiKen-ichi Yoshida
Nov 26, 2013·Nucleic Acids Research·Vincent LombardBernard Henrissat
Dec 5, 2013·Carbohydrate Polymers·Jia ChenDongzhi Wei
Dec 20, 2013·Protein Science : a Publication of the Protein Society·Lujia ZhangDongzhi Wei
Aug 1, 2014·Journal of Agricultural and Food Chemistry·Shaohua WangDongzhi Wei
Citations
Apr 5, 2016·Scientific Reports·Jorge Álvarez-CervantesMiguel Angel Anducho-Reyes
Jul 12, 2016·Biotechnology for Biofuels·Hanen BouraouiMichael J O'Donohue
Sep 17, 2016·Journal of Agricultural and Food Chemistry·Ying YangDongzhi Wei
Apr 15, 2017·Applied Microbiology and Biotechnology·Takayuki KugeMasayuki Inui