Site-specific DNA binding using a variation of the double stranded RNA
binding motif
Kevin M. Connolly, Jonathan M. Wojciak
& Robert T. Clubb
Department of Chemistry and Biochemistry and UCLA-DOE Laboratory of Structural Biology and Genetics, University of California, Los Angeles, 405 Hilgard Ave, Los Angeles, California 90095, USA.
The integrase family of site-specific recombinases catalyze a diverse
array of DNA rearrangements in archaebacteria, eubacteria and yeast. The solution
structure of the DNA binding domain of the integrase protein from the conjugative
transposon Tn916 has been determined using NMR spectroscopy. The structure
provides the first insights into distal site DNA binding by a site-specific
integrase and reveals that the N-terminal domain is structurally similar to
the double stranded RNA binding domain (dsRBD). The results of chemical shift
mapping experiments suggest that the integrase protein interacts with DNA
using residues located on the face of its three stranded -sheet. This
surface differs from the proposed RNA binding surface in dsRBDs, suggesting
that different surfaces on the same protein fold can be used to bind DNA and
RNA.
-sheet. This
surface differs from the proposed RNA binding surface in dsRBDs, suggesting
that different surfaces on the same protein fold can be used to bind DNA and
RNA.
