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Biochemistry (Moscow)

, Volume 76, Issue 1, pp 94–117 | Cite as

Main factors providing specificity of repair enzymes

  • G. A. NevinskyEmail author
Review
  • 60 Downloads

Abstract

Specific and nonspecific DNA complex formation with human uracil-DNA glycosylase, 8-oxoguanine-DNA glycosylase, and apurine/apyrimidine endonuclease, as well as with E. coli 8-oxoguanine-DNA glycosylase and RecA protein was analyzed using the method of stepwise increase in DNA-ligand complexity. It is shown that high affinity of these enzymes to any DNA (10−4–10−8 M) is provided by a large number of weak additive contacts mainly with DNA internucleoside phosphate groups and in a less degree with bases of nucleotide links “covered” by protein globules. Enzyme interactions with specific DNA links are comparable in efficiency with weak unspecific contacts and provide only for one-two orders of affinity (10−1–10−2 M), but these contacts are extremely important at stages of DNA and enzyme structural adaptation and catalysis proper. Only in the case of specific DNA individual for each enzyme alterations in DNA structure provide for efficient adjustment of reacting enzyme atoms and DNA orbitals with accuracy up to 10–15° and, as a result, for high reaction rate. Upon transition from nonspecific to specific DNA, reaction rate (k cat) increases by 4–8 orders of magnitude. Thus, stages of DNA and enzyme structural adaptation as well as catalysis proper are the basis of specificity of repair enzymes.

Key words

mechanism of action repair enzymes uracil-DNA glycosylase apurine-apyrimidine endonuclease 8-oxoguanine-DNA glycosylase RecA protein 

Abbreviations

AP

apurine/apyrimidine

APE

apurine/apyrimidine endonuclease

BER

base excision repair

Fpg

E. coli 8-oxoguanine-DNA glycosylase

hOGG1

human 8-oxoguanine-DNA glycosylase

I50

the compound concentration at which 50% reaction inhibition is observed

IN

HIV integrase

NA

nucleic acids

ON

oligonucleotide

8-oxoG

8-oxoguanine

PN

protein-nucleic

SILC

stepwise increase in DNA-ligand complexity

ss and ds

single- and double-stranded, respectively

scDNA

supercoiled DNA

Topo

DNA topoisomerase I

UDG

uracil-DNA glycosylase

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© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  1. 1.Institute of Chemical Biology and Fundamental MedicineSiberian Branch of the Russian Academy of SciencesNovosibirskRussia

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