A complex prediction: three-dimensional model of the yeast exosome

• Published in: EMBO reports Vol. 3; no. 7; pp. 628 - 635
• Main Authors: Aloy, Patrick, Ciccarelli, Francesca D, Leutwein, Christina, Gavin, Anne-Claude, Superti-Furga, Giulio, Bork, Peer, Böttcher, Bettina, Russell, Robert B
• Format: Journal Article
• Language: English
• Published: Chichester, UK John Wiley & Sons, Ltd 01.07.2002; Blackwell Publishing Ltd; Oxford University Press
• Subjects: Amino Acid Sequence; Exoribonucleases - chemistry; Exoribonucleases - genetics; Exoribonucleases - metabolism; Humans; Macromolecular Substances; Models, Molecular; Molecular Sequence Data; Polyribonucleotide Nucleotidyltransferase - chemistry; Polyribonucleotide Nucleotidyltransferase - genetics; Polyribonucleotide Nucleotidyltransferase - metabolism; Polyribonucleotide Nucleotidyltransferase - ultrastructure; Protein Structure, Quaternary; Protein Structure, Tertiary; Protein Subunits; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - ultrastructure; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Saccharomyces cerevisiae Proteins - ultrastructure; Scientific Reports; Sequence Alignment
• ISSN: 1469-221X; 1469-3178
• DOI: 10.1093/embo-reports/kvf135

We present a model of the yeast exosome based on the bacterial degradosome component polynucleotide phosphorylase (PNPase). Electron microscopy shows the exosome to resemble PNPase but with key differences likely related to the position of RNA binding domains, and to the location of domains unique to the exosome. We use various techniques to reduce the many possible models of exosome subunits based on PNPase to just one. The model suggests numerous experiments to probe exosome function, particularly with respect to subunits making direct atomic contacts and conserved, possibly functional residues within the predicted central pore of the complex.