PEDS Advance Access published online on June 10, 2009
Protein Engineering Design and Selection, doi:10.1093/protein/gzp022
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A structural model for the HAT domain of Utp6 incorporating bioinformatics and genetics
1Departments of Genetics 2Molecular Biophysics and Biochemistry 3Chemistry 4Therapeutic Radiology, Yale University, New Haven, CT 06520, USA
5 To whom correspondence should be addressed. E-mail: susan.baserga{at}yale.edu
The half-a-tetratricopeptide (HAT) repeat motif is of interest because it is found exclusively in proteins that are involved in RNA metabolism. Little is known about structure–function relationships in this class of repeat motif. Here, we present the results of a combined bioinformatics, modeling and mutagenesis study of the HAT domain of Utp6. We have derived a new HAT consensus, delineated its structure-defining residues and, by homology modeling, have placed these residues in a structural context. By considering only HAT motifs from Utp6 proteins, we identified residues that are shared by, and unique to, only this subset of HAT motifs, suggesting a key functional role. Employing both random and directed mutagenesis of the HAT domain in yeast Utp6, we have identified residues whose mutation results in loss of function. By examining these residues in the context of the homology model, we have delineated those that act by perturbing structure and those that more likely have a direct effect on function. Importantly, the residues we predict to have a direct effect on function map together on the tertiary structure, thus defining a potential functional interaction surface.
Keywords: HAT/homology model/RNA processing/Utp6/yeast
Received May 13, 2009; revised May 13, 2009; accepted May 18, 2009.