Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction.
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.
Yajima
Shunsuke
S
Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan. yshun@nodai.ac.jp
Inoue
Sakura
S
Ogawa
Tetsuhiro
T
Nonaka
Takamasa
T
Ohsawa
Kanju
K
Masaki
Haruhiko
H
D000926:Anticodon / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D003087:Colicins / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D018360:Crystallography, X-Ray; D004722:Endoribonucleases / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D004926:Escherichia coli / Q000187:drug effects / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D008958:Models, Molecular; D018716:Molecular Mimicry; D009843:Oligoribonucleotides / Q000737:chemistry; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012333:RNA, Messenger / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity
D000926:Anticodon; D003087:Colicins; D029968:Escherichia coli Proteins; D009843:Oligoribonucleotides; D012333:RNA, Messenger; C515829:deoxyguanylyl-3'-5'-deoxyuridylic acid; D012343:RNA, Transfer; D004722:Endoribonucleases; C515828:colicin E5 protein, E coli