Nucleic Acids Research Advance Access originally published online on March 1, 2007
Nucleic Acids Research 2007 35(6):1908-1918; doi:10.1093/nar/gkm091
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, No. 6 1908-1918
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Novel protein fold discovered in the PabI family of restriction enzymes
1Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan, 2Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo 108-8639, Japan, 3Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, 4Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan, 5Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan and 6Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
*To whom correspondence should be addressed. Tel: +81 3 5449 5326; Fax: +81 3 5449 5422; Email: ikobaya{at}ims.u-tokyo.ac.jp
Received November 20, 2006. Revised February 1, 2007. Accepted February 1, 2007.
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 ß-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.
Present address: Masayuki Kamo, Intercyto Nano Science CO., LTD, Saito Bio-Incubator #1037-7-15, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Orlowski and J. M. Bujnicki Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses Nucleic Acids Res., June 1, 2008; 36(11): 3552 - 3569. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Gasiunas, G. Sasnauskas, G. Tamulaitis, C. Urbanke, D. Razaniene, and V. Siksnys Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family Nucleic Acids Res., February 11, 2008; 36(3): 938 - 949. [Abstract] [Full Text] [PDF]
|
|