2YJY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.210 

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

  • 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 Gene View: PUM1
Go to UniProtKB:  Q14671
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: 2.598 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.796α = 90.00
b = 59.340β = 90.00
c = 344.724γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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