3GIB

Crystal Structure of the Complex of the E. coli Hfq with Poly(A)

Summary for 3GIB

• Entry DOI: 10.2210/pdb3gib/pdb
• Descriptor: Protein hfq, 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3', 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, ... (4 entities in total)
• Functional Keywords: rna binding protein, hfq-rna complex, degradosome component, dna-binding, rna-binding, stress response, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 26444.39

Authors

Link, T.M.,Valentin-Hansen, P.,Brennan, R.G. (deposition date: 2009-03-05, release date: 2009-11-17, Last modification date: 2024-02-21)

Primary citation

Link, T.M.,Valentin-Hansen, P.,Brennan, R.G.
Structure of Escherichia coli Hfq bound to polyriboadenylate RNA
Proc.Natl.Acad.Sci.USA, 106:19292-19297, 2009

PubMed Abstract: Hfq is a small, highly abundant hexameric protein that is found in many bacteria and plays a critical role in mRNA expression and RNA stability. As an "RNA chaperone," Hfq binds AU-rich sequences and facilitates the trans annealing of small RNAs (sRNAs) to their target mRNAs, typically resulting in the down-regulation of gene expression. Hfq also plays a key role in bacterial RNA decay by binding tightly to polyadenylate [poly(A)] tracts. The structural mechanism by which Hfq recognizes and binds poly(A) is unknown. Here, we report the crystal structure of Escherichia coli Hfq bound to the poly(A) RNA, A(15). The structure reveals a unique RNA binding mechanism. Unlike uridine-containing sequences, which bind to the "proximal" face, the poly(A) tract binds to the "distal" face of Hfq using 6 tripartite binding motifs. Each motif consists of an adenosine specificity site (A site), which is effected by peptide backbone hydrogen bonds, a purine nucleotide selectivity site (R site), and a sequence-nondiscriminating RNA entrance/exit site (E site). The resulting implication that Hfq can bind poly(A-R-N) triplets, where R is a purine nucleotide and N is any nucleotide, was confirmed by binding studies. Indeed, Hfq bound to the oligoribonucleotides (AGG)(8), (AGC)(8), and the shorter (A-R-N)(4) sequence, AACAACAAGAAG, with nanomolar affinities. The abundance of (A-R-N)(4) and (A-R-N)(5) triplet repeats in the E. coli genome suggests additional RNA targets for Hfq. Further, the structure provides insight into Hfq-mediated sRNA-mRNA annealing and the role of Hfq in RNA decay.

PubMed: 19889981
DOI: 10.1073/pnas.0908744106

Experimental method

X-RAY DIFFRACTION (2.4 Å)