3MOJ

Structure of the RNA binding domain of the Bacillus subtilis YxiN protein complexed with a fragment of 23S ribosomal RNA

3MOJ の概要

• エントリーDOI: 10.2210/pdb3moj/pdb
• 分子名称: RNA (69-MER), ATP-dependent RNA helicase dbpA (2 entities in total)
• 機能のキーワード: rna, rna recognition motif, rna binding protein, ribosomal rna, rna binding protein-rna complex, rna binding protein/rna
• 由来する生物種: Escherichia coli; 詳細
• 細胞内の位置: Cytoplasm (Probable): P42305
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 32152.04

構造登録者

Hardin, J.W.,Hu, Y.,McKay, D.B. (登録日: 2010-04-22, 公開日: 2010-08-04, 最終更新日: 2024-02-21)

主引用文献

Hardin, J.W.,Hu, Y.X.,McKay, D.B.
Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif.
J.Mol.Biol., 402:412-427, 2010

PubMed Abstract: DEAD-box RNA helicases of the bacterial DbpA subfamily are localized to their biological substrate when a carboxy-terminal RNA recognition motif domain binds tightly and specifically to a segment of 23S ribosomal RNA (rRNA) that includes hairpin 92 of the peptidyl transferase center. A complex between a fragment of 23S rRNA and the RNA binding domain (RBD) of the Bacillus subtilis DbpA protein YxiN was crystallized and its structure was determined to 2.9 A resolution, revealing an RNA recognition mode that differs from those observed with other RNA recognition motifs. The RBD is bound between two RNA strands at a three-way junction. Multiple phosphates of the RNA backbone interact with an electropositive band generated by lysines of the RBD. Nucleotides of the single-stranded loop of hairpin 92 interact with the RBD, including the guanosine base of G2553, which forms three hydrogen bonds with the peptide backbone. A G2553U mutation reduces the RNA binding affinity by 2 orders of magnitude, confirming that G2553 is a sequence specificity determinant in RNA binding. Binding of the RBD to 23S rRNA in the late stages of ribosome subunit maturation would position the ATP-binding duplex destabilization fragment of the protein for interaction with rRNA in the peptidyl transferase cleft of the subunit, allowing it to "melt out" unstable secondary structures and allow proper folding.

PubMed: 20673833
DOI: 10.1016/j.jmb.2010.07.040

実験手法

X-RAY DIFFRACTION (2.902 Å)