Uridine -, crystal structure

From extensive analysis of recombinant proteins, and the crystal structure of A. thaliana protein, detailed reaction mechanisms have been proposed. The ANS reaction likely proceeds via stereospecific hydroxylation of the leucoanthocyanidin (flavan-3,4-cA-diol) at the C-3 to give a flavan-3,3,4-triol, which spontaneously 2,3-dehydrates and isomerizes to 2-flaven-3,4-diol, which then spontaneously isomerizes to a thermodynamically more stable anthocyanidin pseudobase, 3-flaven-2,3-diol (Figure 3.2). The formation of 3-flaven-2,3-diol via the 2-flaven-3,4-diol was previously hypothesized by Heller and Forkmann. The reaction sequence, and the subsequent formation of the anthocyanidin 3-D-glycoside, does not require activity of a separate dehydratase, which was once postulated. Recombinant ANS and uridine diphosphate (UDP)-glucose flavonoid 3-D-glucosyltransferase (F3GT, sometimes... 

Potentially the most interesting crystal structure solved is that of the complex with uridine vanadate (16.40),... 

Nucleoside 2, 3 -cyclic phosphorothioates are prepared by reacting the 5 -acetylnucleoside with triimidazole phosphinsulfide followed by aqueous work-up and deblocking [17]. This procedure is illustrated in Fig. 5 for the exo- and endo-isomers of 2, 3 -cyclic uridine phosphorothioate, 2, 3 -cyclic UMPS, which were first synthesized by Eckstein and associates. The two could be separated because the endo- isomer is crystalline while the other is an oil. After repeated crystallization the pure endo- isomer was obtained and its crystal structure determined, giving its absolute configuration [18]. 

The discovery of these base pairs, which imply the double helical structure of DNA, stimulated a series of crystal structural studies not only of complexes of purines and pyrimidines, but of other complexes involving related molecules and their derivatives. Although we can formulate a large number of possible heterocombinations in matrix form, as shown below these complexes are reluctant to crystallize even when there is spectroscopic evidence of hetero-complex formation in solution. This is presumably because self-(homo)-association is energetically more favorable and only in rare cases were crystals of hetero complexes actually formed. Because of their three hydrogen bonds, G-C complexes form and crystallize more readily. There have been many attempts to crystallize the Watson-Crick A-U base pair, but none was successful and it only formed when the dinucleoside phosphate adenylyl-3,5,-uridine (ApU [536]) or higher oligomers were crystallized (see Part III, Chapter 20). 

Cyclic Dimer Configurations. In 8-bromoinosine [BRINOSlOj the inosine residues are self-associated (Fig. 17.8 a). This is a rare example of self-association in the crystal structures of the nucleosides. Surprisingly, in uridine [BEURID10] (Fig. 17.8b) the CH- 0=C hydrogen bond plays the same role as the NH 0=C interaction in 8-bromoinosine. 

If the crystal structures and hydrogen-bonding patterns of uridine and thymidine and their simpler derivatives are compared with those of cytidine, it becomes obvious that the -NH2 functional group has a characteristic influence. The nucleosides without the -NH2 groups have less than average hydrated crystals, although the one nucleotide represented, uridine-3 -monophosphate, crystallizes as a monohydrate. 

Selected crystal structures of thymidine and its derivatives. The hydrogenbonding patterns of thymidine and its derivatives are comparable to those of the uridine derivatives, but relatively simple and they have a uniformity which is rare. In three of the four structures, infinite chains involving a- and rr-cooperativity occur through the adjacent donor and acceptor groups of the thymine ring. 

Selected crystal structures of cytidlne and its derivatives. The cytidine-related nucleoside and nucleotide crystal structures for which reliable hydrogen-bond patterns can be reported include five nucleotides. Amongst the nucleotides there is more variety than with the uridine compounds. There are three hydrates, four hydrochlorides, and a nitrate. The conjugated NH2 group is always involved as a donor, but never as an acceptor. Several different configurations are observed ... 

Seeman NC, Day RO, Rich A (1975) Nucleic acid-mutagen interactions crystal structure of adenylyl-3, 5 -uridine plus 9-aminoacridine. Nature (Lond) 253 324-326... 

---