Specific interactions between proteins and DNA sequences provide the basic framework through which numerous cellular functions are mediated. In contrast to highly sequence-dependent protein-DNA associations such as those of polymerases, repressors, transcription factors and DNA restriction-modification enzymes with DNA, the DNA repair enzymes comprise a group of proteins which do not interact at specific DNA sequences, but rather monitor DNA for aberrations which may have been caused by thermal radiation or chemical challenge on errors made during DNA replication. This lack of invariant DNA sequence recognition by these enzymes for their substrates does not minimize the requirement for precision in locating and recognizing the DNA aberration. In fact the maintenance of the genetic integrity of the cell is very dependent on these processes. This competing renewal primarily centers on the elucidation of the relationships between the primary, secondary and tertiary structures which are found in one such DNA repair enzyme, T4 endonuclease V and the observed biological and enzymatic functions of that protein. Endonuclease V has been shown by biochemical and genetic analyses to possess four distinctly separable activities: (1) a pyrimidine dimer-specific DNA binding activity; (2) a pyrimidine dimer N-glycosylase activity; (3) an apyrimidinic/apurinic (AP)-endonuclease activity which may be manifest at the site of the N-glycosylase event or which may incise DNA at the site of any missing base; and (4) a salt-sensitive linear diffusion along double-stranded DNA. Models are presented not only for the overall mechanism of action of the enzyme but also for a potential secondary and tertiary structure of the protein. A multidisciplinary approach for elucidating structure-function relationships has been proposed and includes the following: 1) application of the techniques of site-directed mutagenesis to the endonuclease V gene; 2) X-ray crystallography of endonuclease V alone and the enzyme co-crystallized with both unirradiated and irradiated duplex DNA; 3) an understanding of the role that mutant and wild type endonuclease V molecules play in initiating DNA repair in vivo; 4) chemical modification of the enzyme; 5) NMR analyses of endonuclease V; 6) computer modelling of potential secondary structures within endonuclease V; and 7) an examination of potential common structural motifs found within several DNA glycosylases.
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