302
2005–2009; Illanes 2008). Although there are also prosthetic groups that are not
cofactors (e.g. retinal in light receptors), only those prosthetic groups that are
located in the active site of an enzyme are denoted cofactors. Therefore a prosthetic
group is distinguished from a coenzyme in that it stays with the enzyme over many
catalytic cycles, possibly until the enzyme is degraded. The coenzyme, on the other
hand, binds to the enzyme at the beginning of each catalytic cycle and leaves at the
end of it (Union of Pure and Applied Chemistry 2005–2009).
Small portion of the enzyme (active site) is involved in catalysis which is usually
formed by very few amino acid residues. In enzymatic reaction substrate binds to
the enzyme at the active site and produces changes in the distribution of electrons in
its chemical bonds which lead to the reactions that result to the formation of products. The products formed are then released from the enzyme and is ready for the
next catalytic cycle. It is the shape and charge properties of the active site of enzyme
which enable it to bind to a specific substrate molecule, and demonstrate it specificity in catalytic activity (Whitehurst and van Oort 2009). According to the early lock
and key hypothesis proposed by the German chemist Emil Fischer in 1894, the
active site has a unique geometric shape that is complementary to the geometric
shape of the substrate molecule that fits into it. However this rigid hypothesis hardly
explains many experimental evidences of enzyme biocatalysis (Sonkaria et al.
2004). Later on through some techniques such as X-ray crystallography, it became
clear that enzymes are quite flexible but not rigid structures. In the light of this finding, induced-fit theory was proposed by Daniel Koshland in 1958 according to
which the substrate induces a change in the enzyme conformation after binding that
may orient the catalytic groups in a way prone for the subsequent reaction. This
theory has been extensively used to explain enzyme catalysis (Yousef et al. 2003).
Since, it is the active site alone that binds to the substrate. The rest of protein acts to
stabilize the active site and provide an appropriate environment for interaction of
the site with the substrate molecule (Robinson 2015). According to the transitionstate theory, enzyme catalysis is the transition state complementariness, which considers the preferential binding of the transition state rather than the substrate or
product (Benkovic and Hammes-Schiffer 2003).
Classification of Enzymes
Classifying enzymes in different groups based on the type of reaction they catalyze
is a possible way to gain an understanding of the bonds they create or break.
Classification of enzymes is developing constantly and one current issue is that the
recommendations for enzyme classification and nomenclature are inappropriate for
several enzyme groups (e.g. carbohydrate-active enzymes), especially in case of
enzymes with multiple substrate specificity and for isoenzymes. The enzyme classification system is being constantly updated with new enzymes or corrections to
existing entries and the details of recommendations for enzyme classification are
provided. Because of the growing complexity in the naming of enzymes, the
S. A. Rather et al.
2005–2009; Illanes 2008). Although there are also prosthetic groups that are not
cofactors (e.g. retinal in light receptors), only those prosthetic groups that are
located in the active site of an enzyme are denoted cofactors. Therefore a prosthetic
group is distinguished from a coenzyme in that it stays with the enzyme over many
catalytic cycles, possibly until the enzyme is degraded. The coenzyme, on the other
hand, binds to the enzyme at the beginning of each catalytic cycle and leaves at the
end of it (Union of Pure and Applied Chemistry 2005–2009).
Small portion of the enzyme (active site) is involved in catalysis which is usually
formed by very few amino acid residues. In enzymatic reaction substrate binds to
the enzyme at the active site and produces changes in the distribution of electrons in
its chemical bonds which lead to the reactions that result to the formation of products. The products formed are then released from the enzyme and is ready for the
next catalytic cycle. It is the shape and charge properties of the active site of enzyme
which enable it to bind to a specific substrate molecule, and demonstrate it specificity in catalytic activity (Whitehurst and van Oort 2009). According to the early lock
and key hypothesis proposed by the German chemist Emil Fischer in 1894, the
active site has a unique geometric shape that is complementary to the geometric
shape of the substrate molecule that fits into it. However this rigid hypothesis hardly
explains many experimental evidences of enzyme biocatalysis (Sonkaria et al.
2004). Later on through some techniques such as X-ray crystallography, it became
clear that enzymes are quite flexible but not rigid structures. In the light of this finding, induced-fit theory was proposed by Daniel Koshland in 1958 according to
which the substrate induces a change in the enzyme conformation after binding that
may orient the catalytic groups in a way prone for the subsequent reaction. This
theory has been extensively used to explain enzyme catalysis (Yousef et al. 2003).
Since, it is the active site alone that binds to the substrate. The rest of protein acts to
stabilize the active site and provide an appropriate environment for interaction of
the site with the substrate molecule (Robinson 2015). According to the transitionstate theory, enzyme catalysis is the transition state complementariness, which considers the preferential binding of the transition state rather than the substrate or
product (Benkovic and Hammes-Schiffer 2003).
Classification of Enzymes
Classifying enzymes in different groups based on the type of reaction they catalyze
is a possible way to gain an understanding of the bonds they create or break.
Classification of enzymes is developing constantly and one current issue is that the
recommendations for enzyme classification and nomenclature are inappropriate for
several enzyme groups (e.g. carbohydrate-active enzymes), especially in case of
enzymes with multiple substrate specificity and for isoenzymes. The enzyme classification system is being constantly updated with new enzymes or corrections to
existing entries and the details of recommendations for enzyme classification are
provided. Because of the growing complexity in the naming of enzymes, the
S. A. Rather et al.