5ED0

Structure of the Shigella flexneri VapC mutant D7N

Summary for 5ED0

• Entry DOI: 10.2210/pdb5ed0/pdb
• Related: 5ECD
• Descriptor: tRNA(fMet)-specific endonuclease VapC (2 entities in total)
• Functional Keywords: toxin, pin-domain, hydrolase
• Biological source: Shigella flexneri
• Total number of polymer chains: 12
• Total formula weight: 187967.65

Authors

Xu, K.,Dedic, E.,Brodersen, D.E. (deposition date: 2015-10-20, release date: 2016-02-17, Last modification date: 2024-05-08)

Primary citation

Xu, K.,Dedic, E.,Brodersen, D.E.
Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri.
Proteins, 84:892-899, 2016

PubMed Abstract: The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg(2+) -dependent ribonuclease and has been shown to target initiator tRNA(fMet) in vivo. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC forms a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA/RNA hybrid suggests that the Hepes molecule mimics the position of an RNA nucleotide in the VapC active site. Proteins 2016; 84:892-899. © 2016 Wiley Periodicals, Inc.

PubMed: 26833558
DOI: 10.1002/prot.25002

Experimental method

X-RAY DIFFRACTION (2.1 Å)