4W4G

Postcleavage state of 70S bound to HigB toxin and AAA (lysine) codon

This is a non-PDB format compatible entry.

Summary for 4W4G

• Entry DOI: 10.2210/pdb4w4g/pdb
• Descriptor: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (57 entities in total)
• Functional Keywords: ribosome, bacterial toxins, translational control
• Biological source: Proteus vulgaris; More
• Total number of polymer chains: 112
• Total formula weight: 4509262.27

Authors

Schureck, M.A.,Maehigashi, T.,Dunkle, J.A.,Dunham, C.M. (deposition date: 2014-08-14, release date: 2015-10-21, Last modification date: 2023-12-27)

Primary citation

Schureck, M.A.,Dunkle, J.A.,Maehigashi, T.,Miles, S.J.,Dunham, C.M.
Defining the mRNA recognition signature of a bacterial toxin protein.
Proc.Natl.Acad.Sci.USA, 112:13862-13867, 2015

PubMed Abstract: Bacteria contain multiple type II toxins that selectively degrade mRNAs bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. Ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (A) site, but how these endonucleases achieve substrate specificity remains poorly understood. Here, we identify the critical features for how the host inhibition of growth B (HigB) toxin recognizes each of the three A-site nucleotides for cleavage. X-ray crystal structures of HigB bound to two different codons on the ribosome illustrate how HigB uses a microbial RNase-like nucleotide recognition loop to recognize either cytosine or adenosine at the second A-site position. Strikingly, a single HigB residue and 16S rRNA residue C1054 form an adenosine-specific pocket at the third A-site nucleotide, in contrast to how tRNAs decode mRNA. Our results demonstrate that the most important determinant for mRNA cleavage by ribosome-dependent toxins is interaction with the third A-site nucleotide.

PubMed: 26508639
DOI: 10.1073/pnas.1512959112

Experimental method

X-RAY DIFFRACTION (3.3 Å)