In silico studies on bacterial xylanase enzyme: Structural and functional insight

Abstract

Xylans are the second most abundant form of hemicelluloses and are the second most abundant polysaccharide in nature after cellulose. To degrade xylan, microbes produce mainly xylanase enzyme. Wide range of microorganisms like fungi, bacteria, yeast, marine algae etc. are capable of producing xylanase. Main source of xylanase is fungi but industrial production of bacterial xylanase is low cost, easy downstream process and high production rate. To understand primary, secondary and tertiary structure of xylanase, in silico composition of amino acids, basic physiological characteristics; viz ., pI, molecular weight, instability index, GRAVY, molar extinction coefficient, secondary structure, presence of functional domain and motifs, phylogenetic tree, salt bridge compositions are determined. In silico study of xylanase focused on 36 different bacterial sources are performed by retrieving FASTA and PDB sequences using RCSB PDB. FASTA and PDB files are proceed further in ExPASy-ProtParam, RAMPAGE, QMEAN, MEME, PSIPRED, InterProScan, MOTIF scan, ERRAT, Peptide cutter, ESBRI and MEGA 7. The instability index range (16.90–38.78) clearly indicates that the protein is highly stable. α- helix mean value (27.11%) infers the protein is dominated by α- helix region. The aliphatic index (39.80–90.68) gives information that the protein is highly thermostable, prevalence by alanine amino acid in aliphatic side chain. No transmembrane domain was found in the protein which confirms the enzyme is extracellular in nature. Ancestor chart analysis confirmed that it is a part of carbohydrate metabolic process and more specifically a member of glycoside hydrolase super family.

In silico characterization of bacterial chitinase: illuminating its relationship with archaeal and eukaryotic cousins

“…The selected bacterial chitinase model was evaluated using the ERRAT server. The error values that fall below 95% are measured in rejection limit [ 38 ]. In Table 3 , ERRAT showed an overall quality factor of 95.085, a result expected for crystallographic models with resolutions > 2.5 Å.…”

Biochemical and Molecular Characterization of a Thermostable Alkaline Metallo-Keratinase from Bacillus sp. Nnolim-K1

“…Notably, binding of metal ions on a protein could significantly increase the pI value of a protein [ 56 ]. Hence, this could be the case for the metallo-keratinase under investigation, since the pI of proteins theoretically suggests their pH optima [ 57 ].…”

“…The instability index computed for KerBNK1 showed that the enzyme is structurally stable in nature (instability index <40) [ 28 , 57 ]. The aliphatic index indicates the degree of thermal stability of a protein and this is wholly dependent on the relative volume of a protein occupied by the aliphatic residues [ 58 ].…”

“…The aliphatic index indicates the degree of thermal stability of a protein and this is wholly dependent on the relative volume of a protein occupied by the aliphatic residues [ 58 ]. The aliphatic index determined for KerBNK1 implied that the enzyme is significantly thermostable [ 57 ]. Multiple sequence alignment of KerBNK1 with other keratinase sequences from the B. cereus group (sensu lato) showed some variations of amino acid residues and the points of dissimilarity among the sequences are indicated with asterisks (*; Figure 8 ).…”

Characteristics of a XIP‐resistant xylanase from Neocallimastix sp. GMLF1 and its advantage in barley malt saccharification

“…Endo‐β‐1,4‐xylanase (EC 3.2.1.8, briefly referred to as xylanase) can degrade the β‐1, 4‐glycosidic bonds within the main chain of xylan randomly, reducing the polymeric degree of xylan and releasing xylooligosaccharides with a small amount of xylose (Nordberg et al ., ; Adiguzela & Adiguzel, ). Xylanases are found to be produced by microorganisms, plants, algaes, insects, molusks, worms, etc, among which bacterial and fungal xylanases are mostly researched (Dutta et al ., ). According to the homology of the amino acid sequence in catalytic domain (Guo et al ., ), most xylanases are classified into the glycoside hydrolase (GH) family 5, 8, 10, 11, 16, 26, 30, 43 and 62 (http://www.cazy.org/).…”