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
  • Primary Citation of Related Structures:  
    2YJY

  • 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 unknown ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUMILIO HOMOLOG 1A, B350Homo sapiensMutation(s): 2 
Gene Names: PUM1KIAA0099PUMH1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14671 (Homo sapiens)
Explore Q14671 
Go to UniProtKB:  Q14671
PHAROS:  Q14671
GTEx:  ENSG00000134644 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14671
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'C, D 10synthetic construct
Protein Feature View
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  • Reference Sequence
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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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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