7D2P

Crystal structure of MazE-MazF (Form-II) from Deinococcus radiodurans

Summary for 7D2P

• Entry DOI: 10.2210/pdb7d2p/pdb
• Descriptor: Endoribonuclease MazF, AbrB/MazE/SpoVT family DNA-binding domain-containing protein (3 entities in total)
• Functional Keywords: mazef toxin-antitoxin system, toxin, antitoxin, endonuclease
• Biological source: Deinococcus radiodurans; More
• Total number of polymer chains: 6
• Total formula weight: 67696.99

Authors

Dhanasingh, I.,Lee, S.H. (deposition date: 2020-09-17, release date: 2021-02-10, Last modification date: 2023-11-29)

Primary citation

Dhanasingh, I.,Choi, E.,Lee, J.,Lee, S.H.,Hwang, J.
Functional and structural characterization of Deinococcus radiodurans R1 MazEF toxin-antitoxin system, Dr0416-Dr0417.
J.Microbiol, 59:186-201, 2021

PubMed Abstract: In prokaryotes, toxin-antitoxin (TA) systems are commonly found. They likely reflect the adaptation of pathogenic bacteria or extremophiles to various unfavorable environments by slowing their growth rate. Genomic analysis of the extremophile Deinococcus radiodurans R1 revealed the presence of eight type II TA systems, including the genes dr0417, dr0660, dr1530, dr0690, and dr1807. Expression of these toxin genes led to inhibition of Escherichia coli growth, whereas their antidote antitoxins were able to recover the growth defect. Remarkably, Dr0417 (DrMazF) showed endoribonuclease activity toward rRNAs as well as mRNAs, as determined by in vivo and in vitro RNA cleavage assays, and this activity was inhibited by Dr0416 (DrMazE). It was also found that the expression of dr0416-0417 module is directly regulated by the DrMazE-MazF complex. Furthermore, this TA module was induced under stress conditions and plays an important role in survival. To understand the regulatory mechanism at the molecular level, we determined the first high-resolution structures of DrMazF alone and of the DrMazE-MazF complex. In contrast with the hetero-hexameric state of typical MazE-MazF complexes found in other species, DrMazE-MazF crystal structure consists of a hetero-trimer, with the DNA-binding domain of DrMazE undergoing self-cleavage at the flexible linker loop. Our structure revealed that the unique residue R54 provides an additional positive charge to the substrate-binding pocket of DrMazF, its mutation significantly affects the endonuclease activity. Thus, our work reports the unique structural and biochemical features of the DrMazE-MazF system.

PubMed: 33527318
DOI: 10.1007/s12275-021-0523-z

Experimental method

X-RAY DIFFRACTION (2.07 Å)