Principles of Protein Structure - H. Schulz 1982

Protein–ligand interactions
Nucleotide-binding sites
Nucleotide-binding sites in other proteins

Many Cofactors contain adenosine residues. In NAD-dependent dehydrogenases, the binding subsite for the adenosine moiety is exceptionally well conserved. Various other protein cofactors, such as ATP, NADP, FAD, coenzyme A, S-adenosylmethionine, PAPS, and deoxyadenosylcobalamin, also feature adenosine fragments. Therefore, It is important to determine to what extent generalizations regarding NAD binding in dehydrogenases can be extended to other nucleotide–Structure/156.html">Protein Interactions.

Many nucleotide-binding Proteins exhibit similarities to NAD-dependent dehydrogenases. All structurally characterized nucleotide-binding proteins display a certain degree of resemblance to dehydrogenases. Phosphoglycerate kinase [235, 310, 311] contains a domain with the same ß-sheet topology (Sec. 9.6) as the NAD-binding domain, and the adenosine moiety of the ATP cofactor binds in a position corresponding to that of the NAD adenosine residue in dehydrogenases.

In adenylate kinase, the binding sites for the ATP and AMP substrates [665] occupy positions close to that of the ß-sheet in NAD dehydrogenases; the ß-sheets in this case also share similar topologies [255]. From a topological standpoint, the Location of ATP in adenylate kinase corresponds precisely to THE POSITION OF the adenosine-containing portion of NAD in Lactate dehydrogenase. On the other hand, the arrangement of AMP in adenylate kinase corresponds geometrically, but not topologically, to the position of nicotinamide in lactate dehydrogenase. This topological non-equivalence is because ATP and AMP form contacts beneath the region connecting ß-sheets A and B, rather than above it, as shown in Fig. 7.7. The adenine of ATP appears to be hydrogen-bonded to the phenolic OH group of Tyr-95 in adenylate kinase; the isofunctional residue in LDH is Tyr-85. Analogies between LDH and adenylate kinase are also evident in the (pyro)phosphate-binding subsite. Furthermore, both proteins undergo major conformational changes upon nucleotide binding at the respective positions [665].

In flavodoxin, the binding site for the flavin mononucleotide (FMN) prosthetic group is equivalent to the site of the NAD nicotinamide moiety in dehydrogenases [229]. When FMN is superimposed on nicotinamide, the chain folds of flavodoxin and the NAD-binding domain of LDH match almost entirely [91].

In Dihydrofolate Reductase and Glutathione reductase, NADP binds to domains containing ß-sheets of different topologies. Several other proteins compared with the NAD-binding domain are described in [91, 254, 683]. Among them, proteins specific for NADP are of the greatest interest. To the same extent that NAD is typical of catabolic Enzymes, NADP is characteristic of anabolic enzymes. There are two structurally characterized enzymes featuring NADP as a cofactor: dihydrofolate reductase [308] and glutathione reductase [124].

In dihydrofolate reductase, the helices and ß-pleated sheets of the NADP-binding site share certain features with the corresponding elements of the LDH NAD-binding site. However, the topology and chain folding in these two enzymes are entirely different. Glutathione reductase possesses an NAD-binding domain with a parallel ß-sheet in the center [124]. This ß-sheet contains a Rossmann fold that binds the adenosine residue of NADP in a position corresponding to the equivalent site in dehydrogenases. There is no analogous Rossmann fold for the nicotinamide moiety of NADP. Glutathione reductase incorporates FAD as a prosthetic group. Here, too, the adenosine fragment of FAD is attached to a structural element resembling a Rossmann fold.

Certain proteinases degrade the apoproteins of nucleotide-binding enzymes. Long before researchers discovered the common properties of nucleotide-binding proteins [91], these properties were exploited by other naturally occurring agents. These include, in particular, proteinases that specifically degrade the apoproteins of nucleotide-binding enzymes [684]. Another interesting example is salicylate, a compound found in certain plants that also serves as the active principle of aspirin. In both Alcohol dehydrogenase [685] and adenylate kinase [665], salicylate binds as a (weak) inhibitor to the functional groups normally utilized for binding the adenosine residues of NAD and ATP, respectively.