April Journal-2009.p65 - Association of Biotechnology and Pharmacy

Current Trends in Biotechnology and Pharmacy
Vol. 3 (2) 210-218, April 2009. ISSN 0973-8916
211
contributing to the carbon cycle and the natural
decomposition of biomass. Biodegradation and
carbon cycle impact the environment because
nutrients and more usable compounds are
available for other organisms to feed on. This
bacterium degrades the cellulosic materials by a
large multi-enzymes system called the
“cellulosome”. The cellulosome is a complicated
protein complex consisting of nearly 20 different
catalytic subunits or glycoside hydrolases ranging
in size from about 40 to 180 kDa with a total
molecular weight in millions. The database for
glycoside hydrolases is available at website (http:/
/www.cazy.org/fam/acc_GH.html) (2), that
contains classification of glycoside hydrolases in
the families based on amino acid sequence
similarities: i) reflects the structural features of
these enzymes ii) helps to reveal the evolutionary
relationships between these enzymes iii) provides
a convenient tool to derive mechanistic
information. According to the glycoside hydrolase
classification system, several families GH3, GH39
and GH43 exhibit â-xylosidase activity (3,4,5,6,7).
The IUBMB enzyme nomenclature of glycoside
hydrolases is based on their substrate specificity
and occasionally on their molecular mechanism;
such a classification does not reflect the structural
features of these enzymes. Family 39 glycoside
hydrolases (EC:3.2.1.—) are group of enzymes
that hydrolyze the glycosidic bond between two
or more carbohydrates, or between a
carbohydrate and a non-carbohydrate moiety. The
known activities of GH39 are: i) á-L-iduronidase
(EC:3.2.1.76) and ii) â-xylosidase (EC:3.2.1.37).
In most cases, the hydrolysis of the glycosidic
bond is performed by two catalytic residues of
the enzyme vis-a-vis a general acid residue
(proton donor) and a basic residue. Depending
on the spatial position of these catalytic residues,
hydrolysis occurs via overall retention of the
anomeric configuration (8).
MODELLER is used for homology and
comparative modelling of protein threedimensional
structures (9,10). MODELLER
implements comparative protein structure
modelling by satisfaction of spatial restraints
(11,12). It can perform many additional tasks,
including de novo modelling of loops in protein
structures, optimization of various models of
protein structure with respect to a flexibly defined
objective function, multiple alignments of protein
sequences and/or structures, clustering, searching
of sequence databases, comparison of protein
structures. G.N. Ramachandran used computer
models of small polypeptides to systematically vary
phi and ψ with the objective of finding stable
conformations (13). For each conformation, the
structure was examined for close contacts
between atoms. Atoms were treated as hard
spheres with dimensions corresponding to their
van der Waals radii. Therefore, φ and ø angles
which cause spheres to collide correspond to
sterically disallowed conformations of the
polypeptide backbone. In a Ramachandran plot
(13), the core or allowed regions are the areas in
the plot show the preferred regions for psi/phi
angle pairs for residues in a protein (14).
Presumably, if the determination of protein
structure is reliable, most pairs will be in the
favoured regions of the plot and only a few will
be in “disallowed” regions. (14,15). Extensive
scientific work on C. thermocellum has been done
on the genes that control cellulose degradation.
Over 100 genes are involved in encoding proteins
involved in cellulose degradation. This research
is essential for future development of conversion
of biomass into energy that can be achieved by
understanding the genes encoding the cellulose
degrading proteins and how their expressions are
regulated. Cellulose degrading ability of C.
thermocellum can be manipulated and amplified
as a mass energy source. In the present study the
sequence analysis and homology based 3-
dimensioanl structure prediction of family 39
glycoside hydrolase (CtGH39) from Clostridium
thermocellum using above bioinformatics tools
Ahmed et al