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Published online before print November 21, 2003, 10.1101/gad.1109003
GENES & DEVELOPMENT 17:2875-2888, 2003
©2003 by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/ $5.00
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RESEARCH PAPER

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor

Jill M. Bolduc1, P. Clint Spiegel1, Piyali Chatterjee2, Kristina L. Brady2, Maureen E. Downing2, Mark G. Caprara2, Richard B. Waring3 and Barry L. Stoddard1,4

1 Fred Hutchinson Cancer Research Center, Division of Basic Sciences, Seattle, Washington 98109, USA , 2 Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106-4960, USA , 3 Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, USA

We determined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease, termed the I-AniI maturase, in complex with its DNA target at 2.6 Å resolution. The structure demonstrates the remarkable structural conservation of the {beta}-sheet DNA-binding motif between highly divergent enzyme subfamilies. DNA recognition by I-AniI was further studied using nucleoside deletion and DMS modification interference analyses. Correlation of these results with the crystal structure provides information on the relative importance of individual nucleotide contacts for DNA recognition. Alignment and modeling of two homologous maturases reveals conserved basic surface residues, distant from the DNA-binding surface, that might be involved in RNA binding. A point mutation that introduces a single negative charge in this region uncouples the maturase and endonuclease functions of the protein, inhibiting RNA binding and splicing while maintaining DNA binding and cleavage.

[Keywords: Homing endonuclease; maturase; group I intron; crystal structure; DNA binding]

Received May 2, 2003; revised version accepted September 24, 2003.

Article published online ahead of print. Article and publication date are at http://www.genesdev.org/cgi/doi/10.1101/gad.1109003.

4 Corresponding author.
E-MAIL bstoddar{at}fhcrc.org; FAX (206) 667-6877.


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