A complex prediction: three-dimensional model of the yeast exosome.
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.
Aloy
Patrick
P
EMBL, Meyerhofstrasse, Heidelberg, Germany.
Ciccarelli
Francesca D
FD
Leutwein
Christina
C
Gavin
Anne-Claude
AC
Superti-Furga
Giulio
G
Bork
Peer
P
Bottcher
Bettina
B
Russell
Robert B
RB
D000595:Amino Acid Sequence; D005095:Exoribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D046911:Macromolecular Substances; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011117:Polyribonucleotide Nucleotidyltransferase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D021122:Protein Subunits; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics / Q000648:ultrastructure; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D016415:Sequence Alignment
D046911:Macromolecular Substances; D021122:Protein Subunits; D029701:Saccharomyces cerevisiae Proteins; D011117:Polyribonucleotide Nucleotidyltransferase; D005095:Exoribonucleases