300
An International Commission on enzymes was established by the International
Union of Biochemistry [now termed the International Union of Biochemistry and
Molecular Biology (IUBMB)] in 1956 to address the problems of enzyme classification and nomenclature based on the overall chemical transformation they catalyze. Enzymes are now named and classified systematically with an EC number to
a four level hierarchical description depending on the overall chemical transformation of substrates into products (Cuesta et al. 2015). The EC classification is still
made on the basis of the main reaction catalyzed. The EC denotes the six classes of
enzymes based on general type of reaction being carried out including (EC-1) oxidoreductases, (EC-2) transferases, (EC-3) hydrolases, (EC-4) lyases, (EC-5) isomerases, and (EC-6) ligases, where EC stands for Enzyme Commission (Kumar
et al. 2015).
Enzyme function is intrinsically linked to its structure, determining how it performs substrate binding, catalysis and regulation. The amino acid-based enzymes
are globular proteins that range in size from <100 to >2000 amino acid residues.
These amino acids can be arranged into polypeptide chains that are folded and bent
to form a specific three-dimensional structure (Robinson 2015). Some of the amino
acids in enzymes are involved in binding ligands (substrates, intermediates, products, organic cofactors, metal cofactors or allosteric regulators) and some are
actively involved in catalysis by interacting with the substrate, intermediate or product of the reaction (Soding et al. 2005). The structures of enzymes can be elucidating by techniques such as spectroscopic methods, X-ray crystallography and more
recently, multidimensional NMR methods. The X-ray crystallography has been the
most widely used technique for structural characterization of enzymes. The first
enzyme to be crystallized and its structure successfully solved was chicken egg
lysozyme in 1965. NMR spectroscopy is a powerful tool for elucidating the structure–function relationships of enzymes. It yields detailed information regarding
structure of enzyme and the specific ligands which bind to the enzyme. The structure of the ligands at the binding sites of enzymes and the structure of enzyme–
ligand complexes can also be obtained, as well as the dynamics of the ligand and the
associated structure of the protein binding site (Monasterio 2014). The aim of this
chapter is to present and update the existing knowledge about basic principles of
enzymes such as proteinaceous nature and substrate binding, detailed description of
the enzyme classification and structural characterization.
Proteinaceous Nature of Enzymes and Substrate Binding
All enzymes are proteins made up of amino acids linked together by peptide bonds
except small group of RNAase molecules (Bhatia 2018). The structure and reactivity of a protein depends its amino acid sequence, called primary structure, which is
genetically determined by the deoxyribonucleotide sequence in the structural gene
that codes for it (Illanes 2008). The deoxyribonucleotide sequence is transcribed
into a mRNA molecule. The mRNA molecule upon reaching the ribosome of cell is
S. A. Rather et al.
An International Commission on enzymes was established by the International
Union of Biochemistry [now termed the International Union of Biochemistry and
Molecular Biology (IUBMB)] in 1956 to address the problems of enzyme classification and nomenclature based on the overall chemical transformation they catalyze. Enzymes are now named and classified systematically with an EC number to
a four level hierarchical description depending on the overall chemical transformation of substrates into products (Cuesta et al. 2015). The EC classification is still
made on the basis of the main reaction catalyzed. The EC denotes the six classes of
enzymes based on general type of reaction being carried out including (EC-1) oxidoreductases, (EC-2) transferases, (EC-3) hydrolases, (EC-4) lyases, (EC-5) isomerases, and (EC-6) ligases, where EC stands for Enzyme Commission (Kumar
et al. 2015).
Enzyme function is intrinsically linked to its structure, determining how it performs substrate binding, catalysis and regulation. The amino acid-based enzymes
are globular proteins that range in size from <100 to >2000 amino acid residues.
These amino acids can be arranged into polypeptide chains that are folded and bent
to form a specific three-dimensional structure (Robinson 2015). Some of the amino
acids in enzymes are involved in binding ligands (substrates, intermediates, products, organic cofactors, metal cofactors or allosteric regulators) and some are
actively involved in catalysis by interacting with the substrate, intermediate or product of the reaction (Soding et al. 2005). The structures of enzymes can be elucidating by techniques such as spectroscopic methods, X-ray crystallography and more
recently, multidimensional NMR methods. The X-ray crystallography has been the
most widely used technique for structural characterization of enzymes. The first
enzyme to be crystallized and its structure successfully solved was chicken egg
lysozyme in 1965. NMR spectroscopy is a powerful tool for elucidating the structure–function relationships of enzymes. It yields detailed information regarding
structure of enzyme and the specific ligands which bind to the enzyme. The structure of the ligands at the binding sites of enzymes and the structure of enzyme–
ligand complexes can also be obtained, as well as the dynamics of the ligand and the
associated structure of the protein binding site (Monasterio 2014). The aim of this
chapter is to present and update the existing knowledge about basic principles of
enzymes such as proteinaceous nature and substrate binding, detailed description of
the enzyme classification and structural characterization.
Proteinaceous Nature of Enzymes and Substrate Binding
All enzymes are proteins made up of amino acids linked together by peptide bonds
except small group of RNAase molecules (Bhatia 2018). The structure and reactivity of a protein depends its amino acid sequence, called primary structure, which is
genetically determined by the deoxyribonucleotide sequence in the structural gene
that codes for it (Illanes 2008). The deoxyribonucleotide sequence is transcribed
into a mRNA molecule. The mRNA molecule upon reaching the ribosome of cell is
S. A. Rather et al.