3V7E

Crystal structure of YbxF bound to the SAM-I riboswitch aptamer

Summary for 3V7E

• Entry DOI: 10.2210/pdb3v7e/pdb
• Related: 3V7Q
• Descriptor: Ribosome-associated protein L7Ae-like, SAM-I riboswitch aptamer with an engineered helix P3, COBALT HEXAMMINE(III), ... (6 entities in total)
• Functional Keywords: rna-protein complex, riboswitch, k-turn, l7ae-like, a member of the l7ae/l30e superfamily, unknown function, k-turn motif, ribosomal protein-rna complex, ribosomal protein/rna
• Biological source: Bacillus subtilis; More
• Cellular location: Cytoplasm: P46350
• Total number of polymer chains: 4
• Total formula weight: 102630.07

Authors

Baird, N.J.,Zhang, J.,Hamma, T.,Ferre-D'Amare, A.R. (deposition date: 2011-12-21, release date: 2012-03-07, Last modification date: 2023-09-13)

Primary citation

Baird, N.J.,Zhang, J.,Hamma, T.,Ferre-D'Amare, A.R.
YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.
Rna, 18:759-770, 2012

PubMed Abstract: The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) ~270 nM and ~2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.

PubMed: 22355167
DOI: 10.1261/rna.031518.111

Experimental method

X-RAY DIFFRACTION (2.8 Å)