Abstract—This study aimed to determine the biochemical properties of the AbfA variant (Q46R; D205E; K285E) also the correlation between change in biochemical properties and its tertiary structure modification. The enzyme expressed in E. coli BL21 (DE3)/ pBM5abf variant was partially purified by heat treatment for 1 hour at 70oC. The partially purified enzyme was characterized for its biochemical properties. Protein tertiary structure model was built by homology modeling method using Geobacillus stearothermophilus T-6 α-L-arabinofuranosidase crystal structure (PDB: 1PZ3) as template. The protein structure model then subjected for in silico study. Partial purification showed an increase of purity by 17.60 fold. The partially purified enzyme showed optimum activity towards p-nitrophenyl-α-L-arabinofuranoside (pNPA) at pH 7 and 70^oC. AbfA variant (Q46R; D205E; K285E) was stable for 24 hours at pH 6-9 (at 4^oC) and lost almost 70% of its activity on 16 hours incubation at 70^oC. Compared to its wildtype, AbfA variant (Q46R; D205E; K285E) showed decrease on thermostability. Superimpose of AbfA variant (Q46R; D205E; K285E) to its wildtype showed RMSD 0.05. Tertiary structure assessment showed that mutations caused reduction of 3 Hydrogen bonds and 5 Van der Waals interactions also formation of 1 salt bridge and 1 weak electrostatic interaction. In silico analysis of AbfA variant (Q46R; D205E; K285E) protein model revealed that the decrease on thermostability was related to the reduction of some non covalent interactions especially Hydrogen bonds and Van der Waals interaction, due to modification in AbfA variant (Q46R; D205E; K205E) structure.

Index Terms—Biochemical properties, α-L-arabinofuranosidase (AbfA), in silico, non covalent interaction.

N. N. T. Puspaningsih is with the Department of Chemistry and Laboratory of Proteomic, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia (phone: +62-31- 5922427, e-mail: nyomantri@yahoo.com).
Ratna Melinda, Handoko Darmokoesoemo, and Purkan are with Departement of Chemistry, Universitas Airlangga, 60115, Surabaya, Indonesia.

Cite:Ratna Melinda, Purkan, Handoko Darmokoesoemo, and N. N. T. Puspaningsih, "Characterization of α-L-Arabinofuranosidase (AbfA) Variant (Q46R; D205E; K285E) Biochemical Properties and in Silico Study on the Effect of Mutation to Its Structure," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 3, no. 5, pp. 520-527, 2013.