2YJY

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

Summary for 2YJY

• Entry DOI: 10.2210/pdb2yjy/pdb
• Related: 1IB2 1M8W 1M8X 1M8Y 1M8Z
• Descriptor: PUMILIO HOMOLOG 1, 5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3' (3 entities in total)
• Functional Keywords: rna binding protein-rna complex, nanos response element, rna binding protein/rna
• Biological source: HOMO SAPIENS (HUMAN); More
• Cellular location: Cytoplasm: Q14671
• Total number of polymer chains: 4
• Total formula weight: 87289.36

Authors

Dong, S.,Wang, Y.,Cassidy-Amstutz, C.,Lu, G.,Qiu, C.,Bigler, R.,Jezyk, M.,Li, C.,Hall, T.M.T.,Wang, Z. (deposition date: 2011-05-24, release date: 2011-06-08, Last modification date: 2023-12-20)

Primary citation

Dong, S.,Wang, Y.,Cassidy-Amstutz, C.,Lu, G.,Bigler, R.,Jezyk, M.R.,Li, C.,Hall, T.M.,Wang, Z.
Specific and Modular Binding Code for Cytosine Recognition in Pumilio/Fbf (Puf) RNA-Binding Domains.
J.Biol.Chem., 286:26732-, 2011

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. 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.

PubMed: 21653694
DOI: 10.1074/JBC.M111.244889

Experimental method

X-RAY DIFFRACTION (2.598 Å)