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Site-specific DNA binding using a variation of the double stranded RNA binding motif
K M Connolly1, J M Wojciak, R T Clubb
1Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.
Nature Structural Biology
|July 17, 1998
Summary
Integrase proteins, crucial for DNA rearrangements, bind DNA using a novel surface distinct from RNA-binding surfaces. This finding reveals adaptability in protein structure-function relationships for site-specific recombinases.
Area of Science:
- Molecular Biology
- Structural Biology
- Genetics
Background:
- Integrase family proteins are site-specific recombinases essential for DNA rearrangements in various organisms.
- Understanding their DNA-binding mechanisms is key to deciphering their biological roles.
Purpose of the Study:
- To determine the solution structure of the DNA binding domain of the integrase protein from conjugative transposon Tn916.
- To elucidate the mechanism of distal site DNA binding by this site-specific integrase.
Main Methods:
- Nuclear Magnetic Resonance (NMR) spectroscopy was employed to determine the protein's solution structure.
- Chemical shift mapping experiments were conducted to identify DNA-interacting residues.
Main Results:
- The N-terminal domain of the integrase protein shares structural similarity with the double-stranded RNA binding domain (dsRBD).
- DNA-binding interactions primarily involve residues on the face of the protein's three-stranded beta-sheet.
- This DNA-binding surface is distinct from the proposed RNA-binding surface in dsRBDs.
Conclusions:
- The integrase protein utilizes a unique surface for DNA binding, differing from the canonical RNA-binding surface of dsRBDs.
- This suggests that similar protein folds can employ distinct surfaces for binding different nucleic acid types (DNA vs. RNA).
- Provides novel insights into the distal DNA binding mechanism of site-specific integrases.