1TFK

Ribonuclease from Escherichia coli complexed with its inhibtor protein

Summary for 1TFK

• Entry DOI: 10.2210/pdb1tfk/pdb
• Related: 1TFO
• Descriptor: Colicin D, Colicin D immunity protein, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: protein-protein complex, toxin-toxin inhibitor complex, toxin/toxin inhibitor
• Biological source: Escherichia coli; More
• Total number of polymer chains: 2
• Total formula weight: 21657.60

Authors

Yajima, S.,Nakanishi, K.,Takahashi, K.,Ogawa, T.,Kezuka, Y.,Hidaka, M.,Nonaka, T.,Ohsawa, K.,Masaki, H. (deposition date: 2004-05-27, release date: 2005-03-01, Last modification date: 2024-02-14)

Primary citation

Yajima, S.,Nakanishi, K.,Takahashi, K.,Ogawa, T.,Hidaka, M.,Kezuka, Y.,Nonaka, T.,Ohsawa, K.,Masaki, H.
Relation between tRNase activity and the structure of colicin D according to X-ray crystallography
Biochem.Biophys.Res.Commun., 322:966-973, 2004

PubMed Abstract: Colicin D is a plasmid-encoded proteinaceous toxin which kills sensitive Escherichia coli. Toxicity stems from ribonuclease activity that targets exclusively four isoacceptors of tRNA(Arg) with a cleavage position between 38 and 39 of the corresponding anticodons. Since no other tRNAs with the same sequences at 38 and 39 as tRNA(Arg)s are cleaved, colicin D should be capable of recognizing some higher order structure of tRNAs. We report here two crystal structures of catalytic domains of colicin D which have different N-terminal lengths, both complexed with its cognate inhibitor protein, ImmD. A row of positive charge patches is found on the surface of the catalytic domain, suggestive of the binding site of the tRNAs. This finding, together with our refined tRNase activity experiments, indicates that the catalytic domain starting at position 595 has activity almost equivalent to that of colicin D.

PubMed: 15336558
DOI: 10.1016/j.bbrc.2004.07.206

Experimental method

X-RAY DIFFRACTION (2.1 Å)