skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p

Abstract

Pumilio/FBF (PUF) family proteins are found in eukaryotic organisms and regulate gene expression post-transcriptionally by binding to sequences in the 3' untranslated region of target transcripts. PUF proteins contain an RNA binding domain that typically comprises eight {alpha}-helical repeats, each of which recognizes one RNA base. Some PUF proteins, including yeast Puf4p, have altered RNA binding specificity and use their eight repeats to bind to RNA sequences with nine or ten bases. Here we report the crystal structures of Puf4p alone and in complex with a 9-nucleotide (nt) target RNA sequence, revealing that Puf4p accommodates an 'extra' nucleotide by modest adaptations allowing one base to be turned away from the RNA binding surface. Using structural information and sequence comparisons, we created a mutant Puf4p protein that preferentially binds to an 8-nt target RNA sequence over a 9-nt sequence and restores binding of each protein repeat to one RNA base.

Authors:
; ;  [1]
  1. (NIH)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE
OSTI Identifier:
1006623
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nat. Struct. Mol. Biol.; Journal Volume: 15; Journal Issue: (4) ; 04, 2008
Country of Publication:
United States
Language:
ENGLISH
Subject:
60 APPLIED LIFE SCIENCES; CRYSTAL STRUCTURE; GENES; GENE REGULATION; MUTANTS; NUCLEOTIDES; PROTEINS; RNA; SPECIFICITY; TRANSCRIPTION; YEASTS

Citation Formats

Miller, Matthew T., Higgin, Joshua J., and Hall, Traci M.Tanaka. Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p. United States: N. p., 2008. Web. doi:10.1038/nsmb.1390.
Miller, Matthew T., Higgin, Joshua J., & Hall, Traci M.Tanaka. Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p. United States. doi:10.1038/nsmb.1390.
Miller, Matthew T., Higgin, Joshua J., and Hall, Traci M.Tanaka. Fri . "Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p". United States. doi:10.1038/nsmb.1390.
@article{osti_1006623,
title = {Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p},
author = {Miller, Matthew T. and Higgin, Joshua J. and Hall, Traci M.Tanaka},
abstractNote = {Pumilio/FBF (PUF) family proteins are found in eukaryotic organisms and regulate gene expression post-transcriptionally by binding to sequences in the 3' untranslated region of target transcripts. PUF proteins contain an RNA binding domain that typically comprises eight {alpha}-helical repeats, each of which recognizes one RNA base. Some PUF proteins, including yeast Puf4p, have altered RNA binding specificity and use their eight repeats to bind to RNA sequences with nine or ten bases. Here we report the crystal structures of Puf4p alone and in complex with a 9-nucleotide (nt) target RNA sequence, revealing that Puf4p accommodates an 'extra' nucleotide by modest adaptations allowing one base to be turned away from the RNA binding surface. Using structural information and sequence comparisons, we created a mutant Puf4p protein that preferentially binds to an 8-nt target RNA sequence over a 9-nt sequence and restores binding of each protein repeat to one RNA base.},
doi = {10.1038/nsmb.1390},
journal = {Nat. Struct. Mol. Biol.},
number = (4) ; 04, 2008,
volume = 15,
place = {United States},
year = {Fri Jun 06 00:00:00 EDT 2008},
month = {Fri Jun 06 00:00:00 EDT 2008}
}