3HSB

Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer

Summary for 3HSB

• Entry DOI: 10.2210/pdb3hsb/pdb
• Descriptor: Protein hfq, RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3') (3 entities in total)
• Functional Keywords: sm-like motif, protein-rna complex, rna-binding, stress response, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Bacillus subtilis; More
• Total number of polymer chains: 7
• Total formula weight: 55912.77

Authors

Baba, S.,Someya, T.,Kumasaka, T.,Kawai, G.,Nakamura, K. (deposition date: 2009-06-10, release date: 2010-06-23, Last modification date: 2023-11-01)

Primary citation

Someya, T.,Baba, S.,Fujimoto, M.,Kawai, G.,Kumasaka, T.,Nakamura, K.
Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq
Nucleic Acids Res., 40:1856-1867, 2012

PubMed Abstract: Bacterial Hfq is a protein that plays an important role in the regulation of genes in cooperation with sRNAs. Escherichia coli Hfq (EcHfq) has two or more sites that bind RNA(s) including U-rich and/or the poly(A) tail of mRNA. However, functional and structural information about Bacillus subtilis Hfq (BsHfq) including the RNA sequences that specifically bind to it remain unknown. Here, we describe RNA aptamers including fragment (AG)(3)A that are recognized by BsHfq and crystal structures of the BsHfq-(AG)(3)A complex at 2.2 Å resolution. Mutational and structural studies revealed that the RNA fragment binds to the distal site, one of the two binding sites on Hfq, and identified amino acid residues that are critical for sequence-specific interactions between BsHfq and (AG)(3)A. In particular, R32 appears to interact with G bases in (AG)(3)A. Poly(A) also binds to the distal site of EcHfq, but the overall RNA structure and protein-RNA interaction patterns engaged in the R32 residues of BsHfq-(AG)(3)A differ from those of EcHfq-poly(A). These findings provide novel insight into how the Hfq homologue recognizes RNA.

PubMed: 22053080
DOI: 10.1093/nar/gkr892

Experimental method

X-RAY DIFFRACTION (2.2 Å)