2DFX

Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor

2DFX の概要

• エントリーDOI: 10.2210/pdb2dfx/pdb
• 関連するPDBエントリー: 2DJH
• 分子名称: Colicin-E5, Colicin-E5 immunity protein (3 entities in total)
• 機能のキーワード: alpha/beta protein, protein-inhibitor protein complex, hydrolase
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 24680.58

構造登録者

Yajima, S.,Inoue, S.,Ogawa, T.,Nonaka, T.,Ohsawa, K.,Masaki, H. (登録日: 2006-03-06, 公開日: 2007-01-23, 最終更新日: 2025-04-30)

主引用文献

Yajima, S.,Inoue, S.,Ogawa, T.,Nonaka, T.,Ohsawa, K.,Masaki, H.
Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction
Nucleic Acids Res., 34:6074-6082, 2006

PubMed Abstract: Colicin E5--a tRNase toxin--specifically cleaves QUN (Q: queuosine) anticodons of the Escherichia coli tRNAs for Tyr, His, Asn and Asp. Here, we report the crystal structure of the C-terminal ribonuclease domain (CRD) of E5 complexed with a substrate analog, namely, dGpdUp, at a resolution of 1.9 A. Thisstructure is the first to reveal the substrate recognition mechanism of sequence-specific ribonucleases. E5-CRD realized the strict recognition for both the guanine and uracil bases of dGpdUp forming Watson-Crick-type hydrogen bonds and ring stacking interactions, thus mimicking the codons of mRNAs to bind to tRNA anticodons. The docking model of E5-CRD with tRNA also suggests its substrate preference for tRNA over ssRNA. In addition, the structure of E5-CRD/dGpdUp along with the mutational analysis suggests that Arg33 may play an important role in the catalytic activity, and Lys25/Lys60 may also be involved without His in E5-CRD. Finally, the comparison of the structures of E5-CRD/dGpdUp and E5-CRD/ImmE5 (an inhibitor protein) complexes suggests that the binding mode of E5-CRD and ImmE5 mimics that of mRNA and tRNA; this may represent the evolutionary pathway of these proteins from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD.

PubMed: 17099236
DOI: 10.1093/nar/gkl729

実験手法

X-RAY DIFFRACTION (1.9 Å)