Biopolym. Cell. 1996; 12(1):89-94.
http://dx.doi.org/10.7124/bc.000418
Possible role of individual protein-DNA contacts of Flp site-specific recombinase from Saccharomyces cerevisiae with nucleic bases of Flp-binding element of DNA
1Voziyanov Y. A.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Site-specific recombinase Flp encoded by 2 micron plasmidfrom S. cerevisiae has multiple contacts with nucleic bases of Ftp-binding element of DNA. We present an analysis of relative contribution of these contacts to strength of Ftp-protein binding to DNA, and of the peculiarities of their distribution at major and minor grooves of DNA. The contacts of Flp-protein with Ftp-binding element of DNA have been divided into three groups depending on their contribution in strength of Flp-protein binding to DNA. It has been suggested that Flp-protein uses the third group of contacts (they make the least contribution to strength of Flp-protein binding to DNA) along with minor groove contacts for initial discrimination between different DNA sequences. It has been shown that Flp-protein has contacts with nucleic bases in minor groove at opposite sides of DNA, so Flp-protein probably wraps DNA.
Full text: (PDF, in Russian)

References

[1] Futcher AB. Copy number amplification of the 2 micron circle plasmid of Saccharomyces cerevisiae. J Theor Biol. 1986;119(2):197-204.
[2] Volkert FC, Broach JR. Site-specific recombination promotes plasmid amplification in yeast. Cell. 1986;46(4):541-50.
[3] Broach JR, Volkert FC. Circular plasmids in yeasts. The Molecular Biology of the yeast Saccharomyces: Genome dynamics, protein synthesis, and energetics. New York: CSH Laboratory, 1991: 291-331.
[4] Sadowski PD. Site-specific genetic recombination: hops, flips, and flops. FASEB J. 1993;7(9):760-7.
[5] Panigrahi GB, Sadowski PD. Interaction of the NH2- and COOH-terminal domains of the FLP recombinase with the FLP recognition target sequence. J Biol Chem. 1994;269(14):10940-5.
[6] Argos P, Landy A, Abremski K, Egan JB, Haggard-Ljungquist E, Hoess RH, Kahn ML, Kalionis B, Narayana SV, Pierson LS 3rd, et al. The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 1986;5(2):433-40.
[7] Freemont PS, Lane AN, Sanderson MR. Structural aspects of protein-DNA recognition. Biochem J. 1991;278 ( Pt 1):1-23.
[8] Bruckner RC, Cox MM. Specific contacts between the FLP protein of the yeast 2-micron plasmid and its recombination site. J Biol Chem. 1986;261(25):11798-807.
[9] Panigrahi GB, Beatty LG, Sadowski PD. The FLP protein contacts both major and minor grooves of its recognition target sequence. Nucleic Acids Res. 1992;20(22):5927-35.
[10] Kimball AS, Kimball ML, Jayaram M, Tullius TD. Chemical probe and missing nucleoside analysis of Flp recombinase bound to the recombination target sequence. Nucleic Acids Res. 1995;23(15):3009-17.
[11] Saxena P, Whang I, Voziyanov Y, Harkey C, Argos P, Jayaram M, Dandekar T. Probing Flp: a new approach to analyze the structure of a DNA recognizing protein by combining the genetic algorithm, mutagenesis and non-canonical DNA target sites. Biochim Biophys Acta. 1997;1340(2):187-204.
[12] Senecoff JF, Rossmeissl PJ, Cox MM. DNA recognition by the FLP recombinase of the yeast 2 mu plasmid. A mutational analysis of the FLP binding site. J Mol Biol. 1988;201(2):405-21.
[13] Parsons RL, Evans BR, Zheng L, Jayaram M. Functional analysis of Arg-308 mutants of Flp recombinase. Possible role of Arg-308 in coupling substrate binding to catalysis. J Biol Chem. 1990;265(8):4527-33.
[14] Seeman NC, Rosenberg JM, Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A. 1976;73(3):804-8.
[15] Kolomiets IN, Kondratyuk IV, Stepanyugin AV, Samoilenko SA, Zheltovsky NV. Influence of methylation of nucleic acid purine bases on their interactions with amino acids through the carboxylic group. J Mol Struct. 1991;250(1):1–11.
[16] Zheltovsky NV, Samoilenko SA, Kondratyuk IV, Kolomiets IN, Stepanyugin AV. Recognition of purine bases and nucleosides by the amino acid carboxylic group. J Mol Struct. 1995;344(1-2):53–62.
[17] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[18] Schwartz CJ, Sadowski PD. FLP recombinase of the 2 microns circle plasmid of Saccharomyces cerevisiae bends its DNA target. Isolation of FLP mutants defective in DNA bending. J Mol Biol. 1989;205(4):647-58. ttp://
[19] Ross W, Landy A. Patterns of lambda Int recognition in the regions of strand exchange. Cell. 1983;33(1):261-72.
[20] Craig NL, Nash HA. E. coli integration host factor binds to specific sites in DNA. Cell. 1984;39(3 Pt 2):707-16.
[21] Nevinski? GA. An important role for weak interactions during the recognition of long DNA and RNA molecules by enzymes. Mol Biol (Mosk). 1995;29(1):16-37.