Nucleotide-metal complexes, coordination structure

The second major type of stereochemical information that can be obtained about phosphotransferases and nucleotidyltransferases is the coordination structure of nucleotide-metal complexes as they are bound at the active sites of enzymes. Two of the simplest coordination complexes of MgATP are shown below to exemplify the stereochemical difference. These are two stereoisomers differing in screw sense in the coordination ring. 

A central question in phosphotransferases and nucleotidyltransferases is the structure of the metal-nucleotide complex which is the true substrate for the enzyme. It is unlikely that all of the possible Mg-ATP complexes could serve as substrates for a given enzyme, but until recently there has been no way to determine which isomer is active. The difficulty is the coordination exchange equilibrium, which is rapidly set up and dynamically maintained in solutions of Mg-ATP. To avoid this problem, metal-nucleotide complexes have been synthesized using coordination exchange-inert metals such as Cr(III) and Co(IIl) in place of Mg(II) [7,60], The resulting complexes are structurally stable and can be separated by chromatographic methods into their coordination isomers and stereoisomers. The isomers can then be investigated as substrates or inhibitors of specific enzymes. 

In contrast to the relatively simple structures incorporating one of the first three binding motifs, the polymeric complex [Cu3(5 -GMP)3(H20)8] has three distinct coordination environments about different Cu + ions. While this complex is unusually sophisticated, the polymeric nature of the material is common for many metal complexes with GMP or IMP, in which inner-sphere binding occurs to both the N-7 atom and phosphate oxygens of a single nucleotide residue, but does not involve the same metal ion. As described in Section 5.5, there are also unusual structures ( open complexes ) of Cu + species and GMP, which involve only inner-sphere metal binding to the phosphate group. 

Metal complexes of pyrimidine nucleotides have been studied much less intensively than those involving purines, undoubtedly reflecting the weaker coordination ability of the pyrimidine N-3 atom, relative to atoms N-7 and N-1 of purines. Nonetheless, the principal structures of such complexes have been determined. " Some of these are described below. 

A second method for studying the coordination structures of active Mg-nucleotide complexes is to use the P-chiral nucleoside thiotriphosphates and various divalent metal ions as substrates. The divalent metal ions form coordination exchange-labile complexes with ATPaS and ATPjSS, but the various metal ions preferentially form coordination bonds with either S or O. In general, the coor-... 

Investigations on structural data of ternary enzyme-ATP-metal ion complexes have recently been published by COHN (1). A refinement of such structural data would be facilitated by a thorough investigation of the coordination chemistry of the respective binary nucleotide-metal ion complexes i. e, of the question How and to what extent do the different parts of the nucleotide ligands - N-heterocyclic and phosphate moieties - interact with a metal ion, if a binary complex is formed in aqueous solution ... 

Molecular mechanics and dynamics studies of metal-nucleotide and metal-DNA interactions to date have been limited almost exclusively to modeling the interactions involving platinum-based anticancer drugs. As with metal-amino-acid complexes, there have been surprisingly few molecular mechanics studies of simple metal-nucleotide complexes that provide a means of deriving reliable force field parameters. A study of bis(purine)diamine-platinum(II) complexes successfully reproduced the structures of such complexes and demonstrated how steric factors influenced the barriers to rotation about the Pt(II)-N(purine) coordinate bonds and interconversion of the head-to-head (HTH) to head-to-tail (HTT) isomers (Fig. 12.4)[2011. In the process, force field parameters for the Pt(II)/nucleotide interactions were developed. A promising new approach involving the use of ab-initio calculations to calculate force constants has been applied to the interaction between Pt(II) and adenine[202]. 

This vitamin possesses the most complex structure of any of the vitamins and is unique in that it has a metallic element, cobalt, in the molecule (Figure 9-19). The molecule is a coordination complex built around a central tervalent cobalt atom and consists of two major parts—a complex cyclic stmcture that closely resembles the porphyrins and a nucleotide-like portion, 5,6-dimethyl-l-(a-D-ribofuranosyl) benzimidazole-3 -phosphate. The phosphate of the nucleotide is esterified with 1-amino-2-propanol this, in turn, is joined by means of an amide bond with the propionic acid side chain of the large cyclic stmcture. A second linkage with the large stmcture is through the coordinate bond between the cobalt atom and one of the nitro-... 

Interactions of the same water molecules with RNA nucleotides (via H-bonding) and metal ions (via inner-sphere coordination) could stabilize specific metal ion-nucleic acid complexes (e.g. in Mg + -tRNA chelates) and also create the possibility for direct proton transfer through a water chain that could play a role in ribozyme-metal ion catalysis and in the mechanism of metal-dependent nucleases and polymerases. Similar types of H-bonds between different nucleotide residues have been found in tRNA tertiary structures, where they provide additional stabilization of tertiary interactions. 

In the stracture of the polymeric complex of Mn + and 5 -CMP, an unusual cytosine inner-sphere coordination complex has been demonstrated involving, rather than N-3, as well as four phosphate oxygen atoms of three different nucleotides and one water oxygen atom. Thus, in the case of CMP binding, it seems clear that can act as a significant metal-binding site alone, or together with N-3 in chelate structures. 

Coordination exchange-inert metal nucleotide complexes have been synthesized, their structural and stereoisomers have been separated by chromatographic and enzymic methods, and their structures have been determined by X-ray crystallography and correlated to their circular dichroism and P NMR spectra. The pure isomers have been tested as substrates for enzymes in place of MgATP or MgADP, and from the results the structures of the enzyme-bound and active isomers have been deduced. The most widely used complexes of this type have been Cr(III)-aquo complexes and Co(III)-ammine complexes such as those shown below. 

Sigel and co-workers have over a number of years investigated the hydrolysis of a variety of nucleoside 5 -triphosphates and the effects of divalent metal ions. A significant result is that for the hydrolysis of e-ATP (e-ATP is l,A -ethenoadenosine 5 -triphosphate) in the presence of both and Cu +, the most active species is a 2 1 complex metal ion e-ATP (122). It was also proposed that a metal ion bound OH ion effected the hydrolysis. The effect of a number of divalent metal ions on the rates of dephosphorylation of a number of nucleotide triphosphates has also been investigated (128). The ability to dephosphorylate ATP decreased in the order Cu " > Cd > Zn " >Ni >Mn + > Mg-It was suggested that since the pH maximum for the hydrolytic reaction for a particular metal ion paralleled the tendency for that metal ion to form hydroxo complexes (i.e., the p a of the coordinated water molecule) that a metal bound hydroxide ion was involved in the reaction. The most reactive species of the pyrimidine triphosphates could be formulated as [M2(NTP)(OH)J, although the structure of the active complex could only be speculated upon. The reactivity of the purine NTPs was attributed to the dimeric species [M2(NTP)2(0H)]. In both cases, however, two divalent metal ions and a bound hydroxide ion seem to be required to activate the NTPs to hydrolysis. 

In this chapter, we will describe the coordination properties of nucleic acids, including the consequences on metal interactions of the polyanionic nature of oligonucleotides and the supra-molecular structure of the double-helix. Types of metal sites found in other structures such as G-quartets and complex RNA folds will be described. Small coordination compounds between metals and nucleotides, the monomeric units of polymeric DNA and RNA, have been widely studied and also are included in this review. While the majority of material included in the review is derived from X-ray crystallographic studies, some information from spectroscopy and other physical methods is included where illuminating. 

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