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Novel protein fold discovered in the PabI family of restriction enzymes.
- Source :
-
Nucleic acids research [Nucleic Acids Res] 2007; Vol. 35 (6), pp. 1908-18. Date of Electronic Publication: 2007 Mar 01. - Publication Year :
- 2007
-
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.
- Subjects :
- Amino Acid Sequence
Archaeal Proteins genetics
Archaeal Proteins metabolism
Binding Sites
Crystallography, X-Ray
DNA chemistry
DNA Mutational Analysis
DNA-Binding Proteins genetics
DNA-Binding Proteins metabolism
Deoxyribonucleases, Type II Site-Specific genetics
Deoxyribonucleases, Type II Site-Specific metabolism
Molecular Sequence Data
Protein Binding
Protein Biosynthesis
Protein Folding
Protein Structure, Secondary
Pyrococcus abyssi enzymology
Sequence Alignment
Archaeal Proteins chemistry
DNA-Binding Proteins chemistry
Deoxyribonucleases, Type II Site-Specific chemistry
Models, Molecular
Subjects
Details
- Language :
- English
- ISSN :
- 1362-4962
- Volume :
- 35
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- Nucleic acids research
- Publication Type :
- Academic Journal
- Accession number :
- 17332011
- Full Text :
- https://doi.org/10.1093/nar/gkm091