Nucleic Acids Research Advance Access published online on July 3, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp537
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Nucleic Acid Enzymes |
Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease
1Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, 2Department of Molecular Biophysics and Biochemistry and 3Department of Chemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA
*To whom correspondence should be addressed. Tel: +1 850 644 6785; Fax: +1 850 644 7244; Email: hong.li{at}fsu.edu
Received May 13, 2009. Revised June 5, 2009. Accepted June 8, 2009.
The RNA splicing and processing endonuclease from Nanoarchaeum equitans (NEQ) belongs to the recently identified (
β)2 family of splicing endonucleases that require two different subunits for splicing activity. N. equitans splicing endonuclease comprises the catalytic subunit (NEQ205) and the structural subunit (NEQ261). Here, we report the crystal structure of the functional NEQ enzyme at 2.1 Å containing both subunits, as well as that of the NEQ261 subunit alone at 2.2 Å. The functional enzyme resembles previously known 2 and 4 endonucleases but forms a heterotetramer: a dimer of two heterodimers of the catalytic subunit (NEQ205) and the structural subunit (NEQ261). Surprisingly, NEQ261 alone forms a homodimer, similar to the previously known homodimer of the catalytic subunit. The homodimers of isolated subunits are inhibitory to heterodimerization as illustrated by a covalently linked catalytic homodimer that had no RNA cleavage activity upon mixing with the structural subunit. Detailed structural comparison reveals a more favorable hetero- than homodimerization interface, thereby suggesting a possible regulation mechanism of enzyme assembly through available subunits. Finally, the uniquely flexible active site of the NEQ endonuclease provides a possible explanation for its broader substrate specificity.