3RF2

Crystal Structure of 30S Ribosomal Protein S8 from Aquifex Aeolicus

Summary for 3RF2

• Entry DOI: 10.2210/pdb3rf2/pdb
• Descriptor: 30S ribosomal protein S8, SULFATE ION (3 entities in total)
• Functional Keywords: ribosomal protein, rna-binding protein, aquifex aeolicus, hyperthermophilic bacterium, ribosome
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 1
• Total formula weight: 19975.27

Authors

Menichelli, E.,Williamson, J.R. (deposition date: 2011-04-05, release date: 2011-11-16, Last modification date: 2024-02-21)

Primary citation

Menichelli, E.,Edgcomb, S.P.,Recht, M.I.,Williamson, J.R.
The Structure of Aquifex aeolicus Ribosomal Protein S8 Reveals a Unique Subdomain that Contributes to an Extremely Tight Association with 16S rRNA.
J.Mol.Biol., 415:489-502, 2012

PubMed Abstract: The assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. The ribosomal protein S8 from Aquifex aeolicus (AS8) is unique in that there is a 41-residue insertion in the consensus S8 sequence. In addition, AS8 exhibits an unusually high affinity for the 16S ribosomal RNA, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than the equivalent interaction from Escherichia coli. Deletion analysis demonstrated that binding to the minimal site on helix 21 occurred at the same nanomolar affinity found for other bacterial species. The additional affinity required the presence of a three-helix junction between helices 20, 21, and 22. The crystal structure of AS8 was solved, revealing the helix-loop-helix geometry of the unique AS8 insertion region, while the core of the molecule is conserved with known S8 structures. The AS8 structure was modeled onto the structure of the 30S ribosomal subunit from E. coli, suggesting the possibility that the unique subdomain provides additional backbone and side-chain contacts between the protein and an unpaired base within the three-way junction of helices 20, 21, and 22. Point mutations in the protein insertion subdomain resulted in a significantly reduced RNA binding affinity with respect to wild-type AS8. These results indicate that the AS8-specific subdomain provides additional interactions with the three-way junction that contribute to the extremely tight binding to ribosomal RNA.

PubMed: 22079365
DOI: 10.1016/j.jmb.2011.10.046

Experimental method

X-RAY DIFFRACTION (2.16 Å)