3QSU

Structure of Staphylococcus aureus Hfq in complex with A7 RNA

Summary for 3QSU

• Entry DOI: 10.2210/pdb3qsu/pdb
• Related: 1KQ1 1KQ2 3GIB 3HSB
• Descriptor: RNA chaperone Hfq, RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3'), ZINC ION, ... (4 entities in total)
• Functional Keywords: hexamer, sm/lsm family, rna chaperone, translational regulator, mrna, srna, cytoplasma, chaperone-rna complex, chaperone/rna
• Biological source: Staphylococcus aureus
• Total number of polymer chains: 16
• Total formula weight: 129429.39

Authors

Brennan, R.,Horstmann, N.,Link, T.M. (deposition date: 2011-02-21, release date: 2012-09-12, Last modification date: 2024-02-21)

Primary citation

Horstmann, N.,Orans, J.,Valentin-Hansen, P.,Shelburne, S.A.,Brennan, R.G.
Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract.
Nucleic Acids Res., 40:11023-11035, 2012

PubMed Abstract: Hfq is a post-transcriptional regulator that plays a key role in bacterial gene expression by binding AU-rich sequences and A-tracts to facilitate the annealing of sRNAs to target mRNAs and to affect RNA stability. To understand how Hfq from the Gram-positive bacterium Staphylococcus aureus (Sa) binds A-tract RNA, we determined the crystal structure of an Sa Hfq-adenine oligoribonucleotide complex. The structure reveals a bipartite RNA-binding motif on the distal face that is composed of a purine nucleotide-specificity site (R-site) and a non-discriminating linker site (L-site). The (R-L)-binding motif, which is also utilized by Bacillus subtilis Hfq to bind (AG)(3)A, differs from the (A-R-N) tripartite poly(A) RNA-binding motif of Escherichia coli Hfq whereby the Sa Hfq R-site strongly prefers adenosine, is more aromatic and permits deeper insertion of the adenine ring. R-site adenine-stacking residue Phe30, which is conserved among Gram-positive bacterial Hfqs, and an altered conformation about β3 and β4 eliminate the adenosine-specificity site (A-site) and create the L-site. Binding studies show that Sa Hfq binds (AU)(3)A ≈ (AG)(3)A ≥ (AC)(3)A > (AA)(3)A and L-site residue Lys33 plays a significant role. The (R-L) motif is likely utilized by Hfqs from most Gram-positive bacteria to bind alternating (A-N)(n) RNA.

PubMed: 22965117
DOI: 10.1093/nar/gks809

Experimental method

X-RAY DIFFRACTION (2.2 Å)