Novel protein fold discovered in the PabI family of restriction enzymes

Ken Ichi Miyazono, Miki Watanabe, Jan Kosinski, Ken Ishikawa, Masayuki Kamo, Tatsuya Sawasaki, Koji Nagata, Janusz M. Bujnicki, Yaeta Endo, Masaru Tanokura, Ichizo Kobayashi

Research output: Contribution to journalArticle

38 Citations (Scopus)

Abstract

Although structures of many DNA-binding proteins have been solved, they fall into a limited number of folds. Here, we describe an approach that led to the finding of a novel DNA-binding fold. Based on the behavior of Type II restriction-modification gene complexes as mobile elements, our earlier work identified a restriction enzyme, R.PabI, and its cognate modification enzyme in Pyrococcus abyssi through comparison of closely related genomes. While the modification methyltransferase was easily recognized, R.PabI was predicted to have a novel 3D structure. We expressed cytotoxic R.PabI in a wheat-germ-based cell-free translation system and determined its crystal structure. R.PabI turned out to adopt a novel protein fold. Homodimeric R.PabI has a curved anti-parallel β-sheet that forms a 'half pipe'. Mutational and in silico DNA-binding analyses have assigned it as the double-strand DNA-binding site. Unlike most restriction enzymes analyzed, R.PabI is able to cleave DNA in the absence of Mg2+. These results demonstrate the value of genome comparison and the wheat-germ-based system in finding a novel DNA-binding motif in mobile DNases and, in general, a novel protein fold in horizontally transferred genes.

Original languageEnglish
Pages (from-to)1908-1918
Number of pages11
JournalNucleic acids research
Volume35
Issue number6
DOIs
Publication statusPublished - 2007 Mar 1
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'Novel protein fold discovered in the PabI family of restriction enzymes'. Together they form a unique fingerprint.

  • Cite this

    Miyazono, K. I., Watanabe, M., Kosinski, J., Ishikawa, K., Kamo, M., Sawasaki, T., Nagata, K., Bujnicki, J. M., Endo, Y., Tanokura, M., & Kobayashi, I. (2007). Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic acids research, 35(6), 1908-1918. https://doi.org/10.1093/nar/gkm091