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Related Experiment Video

Updated: May 9, 2026

Site-Directed Mutagenesis for In Vitro and In Vivo Experiments Exemplified with RNA Interactions in Escherichia Coli

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Published on: February 5, 2019

Hfq binds ribonucleotides in three different RNA-binding sites.

Victoria Murina¹, Natalia Lekontseva, Alexey Nikulin

¹Institute of Protein Research, RAS, Institutskaya 4, Pushchino 142290, Moscow Region, Russian Federation.

Acta Crystallographica. Section D, Biological Crystallography

|July 31, 2013

Summary

The Hfq protein binds RNA using distinct sites. X-ray crystallography revealed how ribonucleotides like ATP, UTP, and CTP interact with Hfq from Pseudomonas aeruginosa, mapping RNA-binding surfaces.

Keywords:

Hfq RNA–protein interactions ribonucleotide–protein complexes

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Area of Science:

Molecular Biology
Structural Biology
Biochemistry

Background:

The Hfq protein is a crucial bacterial RNA-binding factor, forming a hexameric structure.
Hfq protein exhibits distinct RNA-binding surfaces: proximal for mRNA/sRNAs and distal for A-rich sequences.

Purpose of the Study:

To investigate the binding interactions of various ribonucleotides with Hfq from Pseudomonas aeruginosa.
To utilize X-ray crystallography to map ribonucleotide binding sites on the Hfq protein surface.

Main Methods:

X-ray crystallography was employed to determine the structures of Hfq-ribonucleotide complexes.
Analysis of crystal structures to identify the precise locations of bound ribonucleotides on Hfq.

Main Results:

ATP and ADPNP were localized to the distal R-site, a known poly(A) RNA binding site.
UTP was identified at the proximal lateral RNA-binding site.
CTP bound to both the distal R-site and the proximal U-binding site; GTP did not complex with Hfq.

Conclusions:

The study successfully mapped specific ribonucleotide binding sites on the Hfq protein.
X-ray crystallography is a powerful technique for predicting single-stranded RNA-binding sites on protein surfaces.