The Most Important Factors Providing Specificity of Action of Repair Enzymes (review)
Complexing efficiency of specific and nonspecific DNA with human uracil DNA glycosylase, 8-oxoguanine DNA glycosylase, and apurinic/apyrimidinic endonuclease, as well as E. coli 8-oxoguanine DNA glycosylase and RecA protein using the method of step-wise increase in DNA-ligand complexity was analyzed. It is shown that high affinity of all these enzymes to any DNA (10-5-10-8 M) is provided by many weak additive contacts of the enzymes with internucleoside phosphate groups and to less extent with bases of all nucleotide units of DNA covered by protein globules. Efficiency of formation of specific contacts of repair enzymes with nucleotide units of DNA is comparable with that for the weak nonspecific interactions and provide totally only from one to two orders of the affinity (10-1-10-2 M), but these specific contacts are extremely important for the stage of structural adaptation of DNA and enzyme and directly for the catalysis. Only for specific DNA, changes in DNA structure unique for every repair enzyme provide effective adjustment of reacting orbitals of atoms of enzyme and DNA with accuracy of 10-15° and, as a consequence, high rate of the reactions. On going from nonspecific to specific DNA, the rates of reactions are increased (kcat) by 4-8 orders of magnitude. Thus, the stage of adaptation of DNA and enzyme structure and directly the stage of catalysis are responsible for the specificity of action of the repair enzymes.