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Structural analysis of the active site architecture of the VapC toxin from S higella flexneri
Author(s) -
Xu Kehan,
Dedic Emil,
Brodersen Ditlev E.
Publication year - 2016
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25002
Subject(s) - active site , rnase p , shigella flexneri , chemistry , rna , biology , ribonuclease , transfer rna , dimer , stereochemistry , biochemistry , microbiology and biotechnology , escherichia coli , enzyme , gene , organic chemistry
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.