3BX2

Puf4 RNA binding domain bound to HO endonuclease RNA 3' UTR recognition sequence

Summary for 3BX2

• Entry DOI: 10.2210/pdb3bx2/pdb
• Related: 1IB2 1M6W 1M8X 1M8Y 1M8Z 3BWT 3BX3
• Descriptor: HO endonuclease 3' UTR binding sequence, Protein PUF4, SULFATE ION, ... (5 entities in total)
• Functional Keywords: puf4, pumilio, rna binding, ho endonuclease, transcription, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 4
• Total formula weight: 82387.03

Authors

Miller, M.T.,Higgin, J.J.,Hall, T.M.T. (deposition date: 2008-01-11, release date: 2008-03-11, Last modification date: 2024-02-21)

Primary citation

Miller, M.T.,Higgin, J.J.,Hall, T.M.T.
Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p
Nat.Struct.Mol.Biol., 15:397-402, 2008

PubMed 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.

PubMed: 18327269
DOI: 10.1038/nsmb.1390

Experimental method

X-RAY DIFFRACTION (2.84 Å)