4ML0
Crystal structure of E.coli DinJ-YafQ complex
Summary for 4ML0
| Entry DOI | 10.2210/pdb4ml0/pdb |
| Related | 4ML2 4MMG 4MMJ |
| Descriptor | Predicted antitoxin of YafQ-DinJ toxin-antitoxin system, Predicted toxin of the YafQ-DinJ toxin-antitoxin system, SULFATE ION, ... (4 entities in total) |
| Functional Keywords | rhh motif, interferase, toxin-antitoxin complex, toxin/antitoxin |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 16 |
| Total formula weight | 170233.76 |
| Authors | Liang, Y.J.,Gao, Z.Q.,Liu, Q.S.,Dong, Y.H. (deposition date: 2013-09-06, 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 Cited by 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: 24923448DOI: 10.1074/jbc.M114.559773 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
Download full validation report
