2A8K

Structural and Mutational Studies of the Catalytic Domain of Colicin E5a tRNA-Specific Ribonuclease

Summary for 2A8K

• Entry DOI: 10.2210/pdb2a8k/pdb
• Descriptor: Colicin E5, CALCIUM ION (3 entities in total)
• Functional Keywords: ribonuclease, toxin, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 48145.59

Authors

Lin, Y.L.,Elias, Y.,Huang, R.H. (deposition date: 2005-07-08, release date: 2005-09-20, Last modification date: 2024-02-14)

Primary citation

Lin, Y.L.,Elias, Y.,Huang, R.H.
Structural and mutational studies of the catalytic domain of colicin E5: A tRNA-specific ribonuclease
Biochemistry, 44:10494-10500, 2005

PubMed Abstract: Colicin E5 specifically cleaves four tRNAs in Escherichia coli that contain the modified nucleotide queuosine (Q) at the wobble position, thereby preventing protein synthesis and ultimately resulting in cell death. Here, the crystal structure of the catalytic domain of colicin E5 (E5-CRD) from E. coli was determined at 1.5 A resolution. Unexpectedly, E5-CRD adopts a core folding with a four-stranded beta-sheet packed against an alpha-helix, seen in the well-studied ribonuclease T1 despite a lack of sequence similarity. Beyond the core catalytic domain, an N-terminal helix, a C-terminal beta-strand and loop, and an extended internal loop constitute an RNA binding cleft. Mutational analysis identified five amino acids that were important for tRNA substrate binding and cleavage by E5-CRD. The structure, together with the mutational study, allows us to propose a model of colicin E5-tRNA interactions, suggesting the molecular basis of tRNA substrate recognition and the mechanism of tRNA cleavage by colicin E5.

PubMed: 16060658
DOI: 10.1021/bi050749s

Experimental method

X-RAY DIFFRACTION (1.5 Å)