2N2P

Solution structure of a double base-pair inversion mutant of murine tumour necrosis factor alpha CDE-23 RNA

Summary for 2N2P

• Entry DOI: 10.2210/pdb2n2p/pdb
• Related: 2N2O
• NMR Information: BMRB: 25604
• Descriptor: RNA (5'-R(P*GP*CP*AP*UP*GP*UP*UP*UP*AP*GP*UP*GP*UP*CP*UP*AP*AP*AP*CP*GP*GP*UP*U)-3') (1 entity in total)
• Functional Keywords: cde, rna, murine, mutant
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 7343.35

Authors

Codutti, L.,Leppek, K.,Zalesak, J.,Windeisen, V.,Masiewicz, P.,Stoecklin, G.,Carlomagno, T. (deposition date: 2015-05-11, release date: 2015-08-05, Last modification date: 2024-05-15)

Primary citation

Codutti, L.,Leppek, K.,Zalesak, J.,Windeisen, V.,Masiewicz, P.,Stoecklin, G.,Carlomagno, T.
A Distinct, Sequence-Induced Conformation Is Required for Recognition of the Constitutive Decay Element RNA by Roquin.
Structure, 23:1437-1447, 2015

PubMed Abstract: The constitutive decay element (CDE) of tumor necrosis factor α (TNF-α) mRNA (Tnf) represents the prototype of a class of RNA motifs that mediate rapid degradation of mRNAs encoding regulators of the immune response and development. CDE-type RNAs are hairpin structures featuring a tri-nucleotide loop. The protein Roquin recognizes CDE-type stem loops and recruits the Ccr4-Caf1-Not deadenylase complex to the mRNA, thereby inducing its decay. Stem recognition does not involve nucleotide bases; however, there is a strong stem sequence requirement for functional CDEs. Here, we present the solution structures of the natural Tnf CDE and of a CDE mutant with impaired Roquin binding. We find that the two CDEs adopt unique and distinct structures in both the loop and the stem, which explains the ability of Roquin to recognize stem loops in a sequence-specific manner. Our findings result in a relaxed consensus motif for prediction of new CDE stem loops.

PubMed: 26165594
DOI: 10.1016/j.str.2015.06.001

Experimental method

SOLUTION NMR