Amino acid dehydrogenases structure

Structural Features of Amino Acid Dehydrogenases (AADHs)... 

Tabie 7 Number of Amino Acids and Subunit Molecular Weights of Main Amino Acid Dehydrogenases Whose Primary Structures Have Been Determined... 

Extensive developments of the techniques in gene cloning and related fields have enabled rapid determination of the primary structures of amino acid dehydrogenases. In addition, x-ray crystallographic analyses of several amino acid dehydrogenases have been undertaken and revealed their ternary and quaternary structures in detail. 

Extensive research on characteristics and structure of amino acid dehydrogenases reflects their usefulness for application in industry and other fields. In particular, L-amino acids, which are substrates in oxidative deamination and products in reductive amination, are a very important nutrient, and are also starting materials in pharmaceutical compounds. Amino acid dehydrogenases have been used for the stereospecific synthesis of amino acids from achiral substrates, 2-oxo acids, and ammonia, and for analysis of L-amino acids, oxo acids, ammonia, and assay of enzymes of which amino acids and oxo acids are their substrates or products. Some applications of amino acid dehydrogenases are described in this section. 

The crystal structure of the HNL isolated from S. bicolor (SbHNL) was determined in a complex with the inhibitor benzoic acid." The folding pattern of SbHNL is similar to that of wheat serine carboxypeptidase (CP-WII)" and alcohol dehydrogenase." A unique two-amino acid deletion in SbHNL, however, is forcing the putative active site residues away from the hydrolase binding site toward a small hydrophobic cleft, thereby defining a completely different active site architecture where the triad of a carboxypeptidase is missing. 

Figure 17.8 Catal3ftic zinc center of horse liver alcohol dehydrogenase revealed from an X-ray crystallographic structure (PDB file 20HX) [Al-Karadaghi et al., 1994]. The bound NADH cofactor, a molecule of the inhibitor dimethylsulfoxide (DMSO), and the amino acid residues that coordinate the Zn are shown as sticks shaded according to the elements, and the Zn center is shown as a gray sphere, while the protein is shown in thin gray lines.

Figure 3.1 Amino add side-chain groups involved in binding NAD at the active site of an enzyme. The enzyme is glyceraldehyde dehydrogenase. More than 20 amino acids, the position of which in the primary structure is indicated by the number, counting from the N-terminal amino acid, are involved in the binding. This emphasises the complexity of the binding that is responsible for the specificity of the enzyme for NAD (depicted in bold). The molecular structure of nicotinamide adenine dinucleotide (NAD ) provided in Appendix 3.3.

Since the primary structure of a peptide determines the global fold of any protein, the amino acid sequence of a heme protein not only provides the ligands, but also establishes the heme environmental factors such as solvent and ion accessibility and local dielectric. The prevalent secondary structure element found in heme protein architectures is the a-helix however, it should be noted that p-sheet heme proteins are also known, such as the nitrophorin from Rhodnius prolixus (71) and flavocytochrome cellobiose dehydrogenase from Phanerochaete chrys-osporium (72). However, for the purpose of this review, we focus on the structures of cytochromes 6562 (73) and c (74) shown in Fig. 2, which are four-a-helix bundle protein architectures and lend themselves as resource structures for the development of de novo designs. 

The active center of an LDH subunit is shown schematically in Fig. 2. The peptide backbone is shown as a light blue tube. Also shown are the substrate lactate (red), the coenzyme NAD (yellow), and three amino acid side chains (Arg-109, Arg-171, and His-195 green), which are directly involved in the catalysis. A peptide loop (pink) formed by amino acid residues 98-111 is also shown. In the absence of substrate and coenzyme, this partial structure is open and allows access to the substrate binding site (not shown). In the enzyme lactate NAD"" complex shown, the peptide loop closes the active center. The catalytic cycle of lactate dehydrogenase is discussed on the next page. 

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