4MMG

crystal structure of YafQ mutant H87Q from E.coli

Summary for 4MMG

• Entry DOI: 10.2210/pdb4mmg/pdb
• Related: 4ML0 4ML2 4MMJ
• Descriptor: mRNA interferase YafQ, SULFATE ION (3 entities in total)
• Functional Keywords: toxin, antitoxin
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 22778.08

Authors

Liang, Y.J.,Gao, Z.Q.,Liu, Q.S.,Dong, Y.H. (deposition date: 2013-09-09, release date: 2014-06-25, Last modification date: 2024-03-20)

Primary citation

Liang, Y.,Gao, Z.,Wang, F.,Zhang, Y.,Dong, Y.,Liu, Q.
Structural and Functional Characterization of Escherichia coli Toxin-Antitoxin Complex DinJ-YafQ
J.Biol.Chem., 289:21191-21202, 2014

PubMed Abstract: Toxin YafQ functions as a ribonuclease in the dinJ-yafQ toxin-antitoxin system of Escherichia coli. Antitoxin DinJ neutralizes YafQ-mediated toxicity by forming a stable protein complex. Here, crystal structures of the (DinJ)2-(YafQ)2 complex and the isolated YafQ toxin have been determined. The structure of the heterotetrameric complex (DinJ)2-(YafQ)2 revealed that the N-terminal region of DinJ folds into a ribbon-helix-helix motif and dimerizes for DNA recognition, and the C-terminal portion of each DinJ exclusively wraps around a YafQ molecule. Upon incorporation into the heterotetrameric complex, a conformational change of YafQ in close proximity to the catalytic site of the typical microbial ribonuclease fold was observed and validated. Mutagenesis experiments revealed that a DinJ mutant restored YafQ RNase activity in a tetramer complex in vitro but not in vivo. An electrophoretic mobility shift assay showed that one of the palindromic sequences present in the upstream intergenic region of DinJ served as a binding sequences for both the DinJ-YafQ complex and the antitoxin DinJ alone. Based on structure-guided and site-directed mutagenesis of DinJ-YafQ, we showed that two pairs of amino acids in DinJ were important for DNA binding; the R8A and K16A substitutions and the S31A and R35A substitutions in DinJ abolished the DNA binding ability of the DinJ-YafQ complex.

PubMed: 24923448
DOI: 10.1074/jbc.M114.559773

Experimental method

X-RAY DIFFRACTION (1.5 Å)