cellobiose, cellotetraose, cellotetriose, and laminaribiose to find substances that can
be used as a substrate (carbon and nitrogen source) for cellulase (Selvam et al. 2017).
To this aim, they first modeled the 3D structure of the cellulase of Acinetobacter
sp. by homology modeling and confirmed the structural and atomic properties of the
resulting enzyme using the Ramachandran plot. Cellotetraose showed the highest
score (À7.8759 kJ/mol) in terms of Gibbs free energy (ΔG) in binding to cellulase
among those potential substrates analyzed by molecular docking.
Replacing fossil fuels with renewable resources such as lignocellulosic biomass is
an important alternative in obtaining biofuels and fighting climate change. For this
purpose, Gomez and coworkers characterized an endo-β-1,4-xylanase Xyl2 of
Fusarium oxysporum as a promising glycoside hydrolase enzyme for the industrial
degradation of xylan (Gomez et al. 2016). Using molecular docking technique, to
further understand Xyl2 substrate binding and catalytic mechanism, they performed
docking of a β-1,4-xylopyranoside hexasaccharide (XYP6) with the Xyl2 structure.
In the docking experiment performed (pH 7.5), Glu176 and Tyr72 residues of Xyl2
showed catalytically effective conformation, and the lowest energy pose of Xyl2XYP6 complex was in agreement with the hydrolysis of the β-1,4-glycosidic bond.
Increasing the hydrolytic performance of hemicellulases is crucial to degrade
lignocellulosic biomass in second-generation biorefinery. For this purpose, You and
coworkers designed the variant XYL10C-ΔN by removing the N-terminal 66 amino
acids from the construct in order to develop near-perfect xylanase candidates (You
et al. 2018). They found that the enzymatic activity of the most efficient xylanase
variant increased by 1.8-fold and its thermostability remained within the same level
compared to the wild type. In their docking experiment to understand the structurefunction relationship of the enzyme, Asn269, Tyr272, His302, and Arg336 residues
were determined to have been evolutionarily conserved in relation to the substrate
(long-chain xyloheptaose) and were indispensable in substrate-binding.
Thermophilic xylanases are more suitable due to their stability in industrial
applications. In this context, Chauhan and coworkers subjected Bacillus aestuarii
SC-2014 strain to EMS- and MNNG-induced mutagenesis to enhance the xylanase
activity of the enzyme (Chauhan et al. 2020). They cloned, sequenced, and
performed the molecular docking experiment of wild-type and mutant xylanase
gene products to reveal differential atomic interactions of wild-type and mutant
enzyme-binding pockets with their corresponding substrate. As a result, the
H121D mutation (histidine ! aspartic acid) made the binding pocket acidic and
charged and subsequently enhanced the xylanase activity. Furthermore, the Y99K
(tyrosine ! lysine) and the H121D (histidine ! aspartic acid) mutations were
determined to enhance the thermostability of the mutant protein.
Xylan accounts for about 35% of the dry weight of the plant cell wall and is an
important, abundant, and renewable bioresource. Thermophilic xylanases with high
catalytic activity draw attention in the biofuel, food, and feed industries. In this
context, Wang and coworkers produced the recombinant TlXyn11B protein by
cloning the Talaromyces leycettanus JCM12802 GH11 xylanase gene (Tlxyn11B)
in Pichia pastoris GS115 strain (Wang et al. 2017). They obtained high specific
activity (8259 Æ 32 U/mg with beechwood xylan as substrate) and excellent pH
9 Microbial and Bioinformatics Approach in Biofuel Production
287
be used as a substrate (carbon and nitrogen source) for cellulase (Selvam et al. 2017).
To this aim, they first modeled the 3D structure of the cellulase of Acinetobacter
sp. by homology modeling and confirmed the structural and atomic properties of the
resulting enzyme using the Ramachandran plot. Cellotetraose showed the highest
score (À7.8759 kJ/mol) in terms of Gibbs free energy (ΔG) in binding to cellulase
among those potential substrates analyzed by molecular docking.
Replacing fossil fuels with renewable resources such as lignocellulosic biomass is
an important alternative in obtaining biofuels and fighting climate change. For this
purpose, Gomez and coworkers characterized an endo-β-1,4-xylanase Xyl2 of
Fusarium oxysporum as a promising glycoside hydrolase enzyme for the industrial
degradation of xylan (Gomez et al. 2016). Using molecular docking technique, to
further understand Xyl2 substrate binding and catalytic mechanism, they performed
docking of a β-1,4-xylopyranoside hexasaccharide (XYP6) with the Xyl2 structure.
In the docking experiment performed (pH 7.5), Glu176 and Tyr72 residues of Xyl2
showed catalytically effective conformation, and the lowest energy pose of Xyl2XYP6 complex was in agreement with the hydrolysis of the β-1,4-glycosidic bond.
Increasing the hydrolytic performance of hemicellulases is crucial to degrade
lignocellulosic biomass in second-generation biorefinery. For this purpose, You and
coworkers designed the variant XYL10C-ΔN by removing the N-terminal 66 amino
acids from the construct in order to develop near-perfect xylanase candidates (You
et al. 2018). They found that the enzymatic activity of the most efficient xylanase
variant increased by 1.8-fold and its thermostability remained within the same level
compared to the wild type. In their docking experiment to understand the structurefunction relationship of the enzyme, Asn269, Tyr272, His302, and Arg336 residues
were determined to have been evolutionarily conserved in relation to the substrate
(long-chain xyloheptaose) and were indispensable in substrate-binding.
Thermophilic xylanases are more suitable due to their stability in industrial
applications. In this context, Chauhan and coworkers subjected Bacillus aestuarii
SC-2014 strain to EMS- and MNNG-induced mutagenesis to enhance the xylanase
activity of the enzyme (Chauhan et al. 2020). They cloned, sequenced, and
performed the molecular docking experiment of wild-type and mutant xylanase
gene products to reveal differential atomic interactions of wild-type and mutant
enzyme-binding pockets with their corresponding substrate. As a result, the
H121D mutation (histidine ! aspartic acid) made the binding pocket acidic and
charged and subsequently enhanced the xylanase activity. Furthermore, the Y99K
(tyrosine ! lysine) and the H121D (histidine ! aspartic acid) mutations were
determined to enhance the thermostability of the mutant protein.
Xylan accounts for about 35% of the dry weight of the plant cell wall and is an
important, abundant, and renewable bioresource. Thermophilic xylanases with high
catalytic activity draw attention in the biofuel, food, and feed industries. In this
context, Wang and coworkers produced the recombinant TlXyn11B protein by
cloning the Talaromyces leycettanus JCM12802 GH11 xylanase gene (Tlxyn11B)
in Pichia pastoris GS115 strain (Wang et al. 2017). They obtained high specific
activity (8259 Æ 32 U/mg with beechwood xylan as substrate) and excellent pH
9 Microbial and Bioinformatics Approach in Biofuel Production
287