2DVY

Crystal structure of restriction endonucleases PabI

Summary for 2DVY

• Entry DOI: 10.2210/pdb2dvy/pdb
• Descriptor: Restriction endonuclease PabI (1 entity in total)
• Functional Keywords: restriction endonuclease, hydrolase
• Biological source: Pyrococcus abyssi
• Total number of polymer chains: 6
• Total formula weight: 156300.07

Authors

Miyazono, K.,Watanabe, M.,Kamo, M.,Sawasaki, T.,Nagata, K.,Endo, Y.,Tanokura, M.,Kobayashi, I. (deposition date: 2006-08-01, release date: 2007-05-08, Last modification date: 2024-03-13)

Primary citation

Miyazono, K.,Watanabe, M.,Kosinski, J.,Ishikawa, K.,Kamo, M.,Sawasaki, T.,Nagata, K.,Bujnicki, J.M.,Endo, Y.,Tanokura, M.,Kobayashi, I.
Novel protein fold discovered in the PabI family of restriction enzymes
Nucleic Acids Res., 35:1908-1918, 2007

PubMed 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 beta-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 Mg(2+). 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.

PubMed: 17332011
DOI: 10.1093/nar/gkm091

Experimental method

X-RAY DIFFRACTION (3 Å)