2YJY

A specific and modular binding code for cytosine recognition in PUF domains

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Specific and Modular Binding Code for Cytosine Recognition in Pumilio/Fbf (Puf) RNA-Binding Domains.

Dong, S., Wang, Y., Cassidy-Amstutz, C., Lu, G., Bigler, R., Jezyk, M.R., Li, C., Hall, T.M., Wang, Z.

(2011) J Biol Chem 286: 26732

  • DOI: 10.1074/jbc.M111.244889
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are un ...

    Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.

    Organizational Affiliation: 

    Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUMILIO HOMOLOG 1
A, B
350HOMO SAPIENSMutation(s): 2 
Gene Names: PUM1, KIAA0099, PUMH1
Find proteins for Q14671 (Homo sapiens)
Go to UniProtKB:  Q14671
NIH Common Fund Data Resources
PHAROS  Q14671
GTEx  ENSG00000134644
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'C, D10SYNTHETIC CONSTRUCT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.796α = 90
b = 59.34β = 90
c = 344.724γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-08-03
    Changes: Database references, Version format compliance
  • Version 1.2: 2015-10-28
    Changes: Source and taxonomy