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PrfA protein of Bacillus species: Prediction and demonstration of endonuclease activity on DNA

¹ National Centre of Genetic Resources and Biotechnology, Cenargen/Embrapa, Brasília, Brazil, D.F. 70770–900
² Department of Biochemistry, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
³ Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
⁴ Children's Hospital Oakland Research Institute, Oakland, California 94609, USA

Reprint requests to: Daniel J. Rigden, National Centre of Genetic Resources and Biotechnology, Cenargen/Embrapa, Brasília, Brazil, D.F. 70770-900; e-mail: daniel{at}cenargen.embrapa.br; fax: 55 (61)340-3658 or Mark J. Jedrzejas, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA; e-mail: mjedrzejas{at}chori.org; fax: (510) 450-7910.

The prfA gene product of Gram-positive bacteria is unusual in being implicated in several cellular processes; cell wall synthesis, chromosome segregation, and DNA recombination and repair. However, no homology of PrfA with other proteins has been evident. Here we report a structural relationship between PrfA and the restriction enzyme PvuII, and thereby produce models that predict that PrfA binds DNA. Indeed, wild-type Bacillus stearothermophilus PrfA, but not a catalytic site mutant, nicked one strand of supercoiled plasmid templates leaving 5`-phosphate and 3`-hydroxyl termini. This activity, much lower on linear or relaxed circular double-stranded DNA or on single-stranded DNA, is consistent with a role for this protein in chromosome segregation, DNA recombination, or DNA repair.

Keywords: Endonuclease activity; fold recognition; function prediction; homology modeling

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