Glycosylases catalyzed reactions

As noted earlier (compare Table I), studies made using small prochiral substrates gave the first concrete indications that product configuration in some glycosylase-catalyzed reactions does not depend on that of the substrate but is determined topologically by protein structures which determine how incoming cosubstrates approach the catalytic center.26,32,36,45 4S... 

Proposed Subdivision of Glycosylases Based on Structural Features That Dictate the Stereochemical Outcome of Catalyzed Reactions ... 

Some glycosylases are simple glycosylases, which only catalyze the hydrolytic removal of a base to form an abasic site, whereas other glycosylases cleave off the base using a lyase mechanism and catalyze an AP lyase reaction. In this AP lyase... 

Figure 11.7. Enzymatic events leading to removal of DNA damage. The various types of DNA damage are removed by the action of several families of DNA repair enzymes. The result, in many cases, is a region where part of one strand of the double-stranded helix is missing. The empty region is then filled in with new nucleotides in a reaction catalyzed by DNA polymerase. The sequential activities of uracil DNA glycosylase, AP endonuclease, and 2 -deoxyribophosphodi-esterase catal)rze the total removal of uracil residues, as shown. Uracil DNA glycosylase hydrolyzes the uracil base from the DNA. The other two enzymes catalyze the hydrolysis of a phos-phodiester bond, and then the complete removal of the sugar residue. (From Teebor, 1995.)...

Enzyme-catalyzed glycoside cleavages (and syntheses) are considered by Hehre [6,8] to be variants of the same reaction (O Eq. 1), catalyzed by a single type of enzyme, the glycosylases, comprising glycoside hydrolases, glycosyl transferases, phosphorylases and certain lyases. 

The present main focus, however, is not on reactions with anomerically correct glycosyl donors, but on those catalyzed with nonglycosidic substrates lacking proper configuration. These unusual reactions reveal aspects of catalytic behavior long thought to be forbidden for particular types of glycosylases.8 10... 

Stereochemical Course of Reactions Catalyzed by Various Retaining and Inverting Glycosylases With Prochiral Glycosyl Donors... 

Transition-state structures computed from multiple kinetic isotope-effect, data have provided important information on the catalytic mechanisms of glycosylases. This is exemplified by the refined transition-state structures derived by Schramm and his associates and used to probe the hydrolytic reactions catalyzed by nucleosidases and the ADPR (adenosine diphosphori-bosyl) transferase toxins of Vibrio cholerae and Corynebacterium diphthe-... 

Base excision repair (BER). The N-glycosyl linkages of the pmine and pyrimidine bases to the deox-ribose residues of the sugar-phosphate backbone of DNA are subjecf to sponfaneous hydrolysis, one important source of damage to DNA. Similar hydrolytic reactions are catalyzed by DNA glycosylases, which remove many mismatched or damaged bases. " ... 

Figure 13.11 Reaction sequence of the base excision repair pathway. The base excision repair (BER) pathway is exemplified for the uracil excision-repair reactions. Only the lesioned (e.g. uracil) part of one strand nucleotide structure of the dsDNA is shown. The excision of uracil by uracil DNA glycosylase without associated AP-lyase generally follows AP-endonuclease and 5 -deoxyribophosphodiesterase which cleave the nucleotide chain. The repair with N-glycosylase is associated with AP-lyase (P-elimination reaction catalyzed by AP-lyase converts the deoxyribose residue to aldehyde form) and 3 -phosphodiesterase. The single nucleotide gap is filled by DNA polymerase (dCTP is required to replace uracil) and DNA ligase...

Fig. 3. Reactions catalyzed by apurinic/apyrimidinic (AP) endonucleases. An AP endonuclease will generate a 5 -dRP group and a nicked strand when acting on an abasic site. Alternatively, a single-nucleotide gap will be created if the substrate is the / -elimination product of a bifunctional DNA glycosylase.

After the action of AP endonuclease on an abasic site, DNA repair polymerase (polymerase /3 in eukaryotes or polymerase I in bacteria) can remove the dRP group (so-called dRPase activity ) (Allinson etal, 2001). This reaction is catalyzed by the N-terminal domain of polymerase /3 via an imine intermediate, analogous to the AP lyase activity of bifunctional glycosylases (Piersen et al, 1996 Prasad et al, 1998). If this step... 

Werner, R. M., and Stivers, J. T. (2000). Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase Evidence for an oxocarbenium ion-uracil anion intermediate. Biochemistry 39, 14054—14064. 

Zharkov, D. O., Rieger, R. A., Iden, C. R., and Grollman, A. P. (1997). NH2-terminal proline acts as a nucleophile in the glycosylase/AP-lyase reaction catalyzed by... 

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