X-ray crystallography of enzymes

Each macrocydic scaffold can tolerate some variation in zinc binding warhead, with bidentate chelators often providing the highest activity. The importance of the macrocydic scaffold, whether in HDAC inhibitors or other areas of drug discovery, may not always be clear. It is important to compare the activity of macrocycles with linear analogues to define the contributions specific to the macrocycle and this should be ideally backed up by X-ray crystallography of enzyme-inhibitor complexes. 

The successful application of X-ray crystallography of proteins to solution of the structure of lysozyme has been spectacular, but is beyond the scope of this article. However, the enzyme-substrate complexes are of considerable interest, because these substrates and the (structurally similar) inhibitors are carbohydrates. 

An understanding of the molecular basis for regulation of isocitrate dehydrogenase by phosphorylation was facilitated by X-ray crystallography of the phosphorylated enzyme in complex with isocitrate. The crystal structures of mutants of the enzyme in which SerllS had been exchanged for aspartate or glutamate were also solved (Hurley et al., 1990). The structure of the enzyme in complex with the substrate isocitrate revealed the phophorylation site to be localized near isocitrate. SerllS itself binds the substrate directly via a H-bond with the O of isocitrate (fig. 2.13). 

At their most elaborate, epitope mapping techniques can provide detailed information on the amino acid residues in a protein antigen, which are in direct contact with the antibody binding site. X-ray crystallography of antibody-antigen complexes can identify contact residues directly and unequivocally, though not surprisingly in view of the effort required, this method is not in routine use. At the other extreme, demonstration by competition enzyme-linked immunosorbent assay (ELISA) methods that two antibodies bind to different sites on... 

De Simone G (2009) X-Ray crystallography of CA inhibitors and its importance in drug design. In Supuran CT, Winum J-Y (eds) Drug design of zinc-enzyme inhibitors functional, structural, and disease applications. Wiley, Hoboken... 

Attempts to model the structure of the V-dependent bromoperoxidase enzyme have resnlted in the characterization by X-ray crystallography of a great number of VO + complexes having N,N,N,N-donor atoms. The imidazole group is thought to mimic the protein enviromnent and complexes such as [VO(SALIMH)(acac)(MeOH)], [VO(SALIMH)SAL], and [VO(SALIMH)2(EtOH)], have been prepared " (see Vanadium in Biology). 

The rapid technological progress in X-ray crystallography has enabled the structural analysis of numerous enzymes involved in coenzyme biosynthesis. Complete sets of structures that cover all enzymes of a given pathway are available in certain cases such as riboflavin, tetrahydrobiopterin, and folic acid biosynthesis. Stmctures of orthologs from different taxonomic groups have been reported in certain cases. X-ray structures of enzymes in complex with substrates, products, and analogs of substrates, products, or intermediates have been essential for the elucidation of the reaction mechanisms. Structures of some coenzyme biosynthesis enzymes have been obtained by NMR-structure analysis. 

In Chapter 9, we will examine the chemical details of how enzymes function. The first step in obtaining the chemical mechanism of an enzyme is to determine what functional groups are required for enzyme activity. How can we ascertain these functional groups X ray crystallography of the... 

X-ray crystallography of the recombinant rat liver and human enzyme have fleshed out some details of Palmer-Abeles mechanism. The wt enzyme crystallises in an open conformation, which on binding of... 

---