6NY5

Crystal structure of the PUM-HD domain of S. pombe Puf1 in complex with RNA

Summary for 6NY5

• Entry DOI: 10.2210/pdb6ny5/pdb
• Related: 6NWW
• Descriptor: Pumilio domain-containing protein C56F2.08c, RNA (5'-R(P*UP*UP*AP*AP*UP*AP*AP*CP*UP*UP*AP*AP*U)-3'), SULFATE ION, ... (5 entities in total)
• Functional Keywords: puf protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Schizosaccharomyces pombe (Fission yeast); More
• Total number of polymer chains: 3
• Total formula weight: 93846.18

Authors

Qiu, C.,Hall, T.M.T. (deposition date: 2019-02-11, release date: 2019-07-03, Last modification date: 2024-10-30)

Primary citation

Qiu, C.,Dutcher, R.C.,Porter, D.F.,Arava, Y.,Wickens, M.,Hall, T.M.T.
Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity.
Nucleic Acids Res., 47:8770-8784, 2019

PubMed Abstract: PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct architecture and comprise a highly conserved subfamily among fungal species. Puf1/Puf2 proteins contain two types of RNA-binding domain: a divergent PUM-HD and an RNA recognition motif (RRM). They recognize RNAs containing UAAU motifs, often in clusters. Here, we report a crystal structure of the PUM-HD of a fungal Puf1 in complex with a dual UAAU motif RNA. Each of the two UAAU tetranucleotides are bound by a Puf1 PUM-HD forming a 2:1 protein-to-RNA complex. We also determined crystal structures of the Puf1 RRM domain that identified a dimerization interface. The PUM-HD and RRM domains act in concert to determine RNA-binding specificity: the PUM-HD dictates binding to UAAU, and dimerization of the RRM domain favors binding to dual UAAU motifs rather than a single UAAU. Cooperative action of the RRM and PUM-HD identifies a new mechanism by which multiple RNA-binding modules in a single protein collaborate to create a unique RNA-binding specificity.

PubMed: 31294800
DOI: 10.1093/nar/gkz583

Experimental method

X-RAY DIFFRACTION (3.002 Å)