2G0C

Structure of the RNA binding domain (residues 404-479) of the Bacillus subtilis YxiN protein

Summary for 2G0C

• Entry DOI: 10.2210/pdb2g0c/pdb
• Descriptor: ATP-dependent RNA helicase dbpA, SULFATE ION (3 entities in total)
• Functional Keywords: rna recognition motif, hydrolase
• Biological source: Bacillus subtilis
• Cellular location: Cytoplasm : P42305
• Total number of polymer chains: 1
• Total formula weight: 8484.01

Authors

McKay, D.B. (deposition date: 2006-02-11, release date: 2006-04-18, Last modification date: 2024-04-03)

Primary citation

Wang, S.,Hu, Y.,Overgaard, M.T.,Karginov, F.V.,Uhlenbeck, O.C.,McKay, D.B.
The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold.
RNA, 12:959-967, 2006

PubMed Abstract: The YxiN protein of Bacillus subtilis is a member of the DbpA subfamily of prokaryotic DEAD-box RNA helicases. Like DbpA, it binds with high affinity and specificity to segments of 23S ribosomal RNA as short as 32 nucleotides (nt) that include hairpin 92. Several experiments have shown that the 76-residue carboxy-terminal domain of YxiN is responsible for the high-affinity RNA binding. The domain has been crystallized and its structure has been solved to 1.7 Angstroms resolution. The structure reveals an RNA recognition motif (RRM) fold that is found in many eukaryotic RNA binding proteins; the RRM fold was not apparent from the amino acid sequence. The domain has two solvent exposed aromatic residues at sites that correspond to the aromatic residues of the ribonucleoprotein (RNP) motifs RNP1 and RNP2 that are essential for RNA binding in many RRMs. However, mutagenesis of these residues (Tyr404 and Tyr447) to alanine has little effect on RNA affinity, suggesting that the YxiN domain binds target RNAs in a manner that differs from the binding mode commonly found in many eukaryotic RRMs.

PubMed: 16611943
DOI: 10.1261/rna.5906

Experimental method

X-RAY DIFFRACTION (1.7 Å)